date:20121211

Dear Gromacs Users!


I want to study dynamics of solvent burried into the protein interiour
during simulation (to check solvent accessible  area of different
amino acid of my protein). Eg while simulating of Green Fluorescent
protein I'd like to check how much water burried into the beta-can
interiour of that protein ( which can effect chromophore of that
protein for instance).

What Gromacs utilites can be suitable for such analysis?
I've tried to make such study with the g_rdf but I'm not quite sure
about suitability of that tool for my task ( e.g what is the ref_group
as well as first group about which program ask me when i tried g_rdf
-f wild_Chimera_15ns.xtc -s minim.tpr -n index.ndx -cut 0.4 ) ?


Thanks for help

James
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[gmx-users] DNA simulation

2012-12-11 Thread delara aghaie

Dear Gromacs users

I want to simulate dobule strand DNA using gromacs. I have read that I should 
use amber forcefield for DNA simulation and I have crossed a web page 
explaining some parameters which I should change in gromacs package to become 
compatible with this amber force filed. 


1) I want to know that is it possible to use straightly pdb2gmx command on pdf 
file of DNA (taken fron protein data bank) and choose amber forcefiled for 
that? 

2) Are that changes necessary? 


3) If pdb2gmx does not give error how can I make sure about the correctness of 
procedure.
Thanks in advance
Regards D.M

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[gmx-users] Re: Pulling ion - US

2012-12-11 Thread Thomas Schlesier

I would also use the same residue from the pulling for the US.
One thing you should be aware of is the pulling dimension:
Now you have the pull-code only ativated for the z-direction. If you use 
this still in the US the ion can move freely in the xy-plane (freely in 
the sense of what is possible from the surrounding).

One extreme example:
The ion bounds to the protein and somehow (don't ask, think this wont 
happen in reality) and diffses away (in the xy-plane) after a long time 
it's so far away from the protein that the are no interaction with the 
protein and the ion interacts only with the surrounding water. Now you 
don't measure with the US potential the interaction of the ion with the 
protein, but the free diffusion of the ion.
This case wont happen, since the probability that the ion unbounds 
itself from the protein goes down to the cellar. But i hope you get the 
idea what the gerneral problem is. If you the pull-dim in each direction 
this problem wouldn't occur, since the movement of the ion is also 
restrained in the xy-plane.

Am 10.12.2012 21:40, schrieb gmx-users-requ...@gromacs.org:

Would you also specify in each US window specific residue instead of
the whole protein?

Sreven

On Mon, Dec 10, 2012 at 2:47 PM, Steven Neumann  wrote:

>On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul  wrote:

>>
>>
>>On 12/10/12 9:01 AM, Steven Neumann wrote:

>>>
>>>Dear Gmx Users,
>>>
>>>I am pulling away cation from the protein glutamic acid residue with:
>>>
>>>pull= umbrella
>>>pull_geometry   = distance  ; simple distance increase
>>>pull_dim= N N Y
>>>pull_start  = yes   ; define initial COM distance > 0
>>>pull_ngroups= 1
>>>pull_group0 = Protein
>>>pull_group1 = NA
>>>pull_rate1  = 0.01
>>>pull_k1 = 500  ; kJ mol^-1  nm^-2
>>>
>>>I tried different pulling rates and simulation time to pull it 3 nm
>>>away. I tried pull rate of 0.1; 0.01 and 0.001. The interaction is so
>>>strong that the force reaches 600 kJ/mol/nm2 and they do not become
>>>separated - with position restraints protein looses its secondary
>>>structure and is draged by the ion - they do not become separated.
>>>
>>>Would you suggest constant force pulling in this case? Then I will
>>>extract initial coordinates for US windows. Can I use then US with
>>>harmonic potential in windows then and WHAM?
>>>

>>
>>You can generate coordinates in any way you wish.  I would think that,
>>regardless of the pull method, setting pull_group0 to the actual residue to
>>which the ion is coordinated would be significantly more effective than
>>pulling with respect to the entire protein, though it seems rather strange
>>that the dissociation of an ion would cause a protein to unfold.  A stronger
>>force constant in pull_k1 may also help.
>>
>>-Justin

>
>Thank you Justin. That indeed helped.
>
>Steven

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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Peter, thanks for explanations!


Could you tell me is it possible to convert CGenFF output for
hetatomic group to the RTP   (not an itp ) gromac's data ?

I want to simulate in Gromacs ( in charmm 27 ff) qm\mm GFP protein
which is consist of HETTATOMIC chromophore covently bonded to the
polypeptide chain of that protein so
 I need topology for that chromophore ( I can make it by swiss param
or my CGenFF) but I need that topology in the rtp file format to
integrate it to the aminoacids.rtp  of the Charmm27  for further
processing of the entirely GFP by means of  pdb2gmx.

2012/12/8, Peter C. Lai :
> On 2012-12-08 03:20:54AM -0800, James Starlight wrote:
>> 1- on what assumptions that blocks were generated ?
>
> This appears to be a swissparm-specific question. I don't know what
> algorithms it uses to match what are essentially pharmacophores in the new
> molecule with the common individual blocks it finds.
>
>> 2- Why charge in [ atomtypes ]  (zero) differes from  the charges in
>
> Because gromacs ignores charges in [atomtypes], so the easiest thing is to
> just assign all zeros to that column.
>
>> the topology of the same groups? how I can check correctness of charge
>> distribution in such itp files ?
>
> Compare to analogous molecules and see if there are published charges.
> You can also use the building blocks and manually assign charges and see
> what
> you end up with as well. To be totally rigorous, parameterize the structure
>
> using a quantum chemistry package and compare the ab initio charge
> distributions to the ones assigned by SwissParm (or by hand).
>
>> 3- What is sigma andepsilon in the [ atomtypes ] ? :)
>
> LJ interactions in sigma-epsilon form. See gromacs manual section 4.1.1
>
>> 4- Have anybody else used Swiss param for modeling protein-ligands
>> systems? Might it be used with the charmm36 set ?
>>
>
> CHARMM has its own generalized forcefield (CGenFF) for ligands and other
> molecules, although charmm36 may have cAMP in their nucleotides section...
> You can try to also build it using adenine, ribose, and add phosphate.
>
> CGenFF and C36 are interoperable for intermolecular interactions, so if
> using CGenFF to paramterize cAMP you would use ParamChem to assign charges
> and then convert and add the CGenFF forcefield parameters (from the gromacs
> contributions website) to C36. There are mailing list archives that show
> you the script to use to do the CGenFF conversion.
>
>
>
>> James
>>
>> 2012/12/7, Justin Lemkul :
>> >
>> >
>> > On 12/7/12 2:21 PM, James Starlight wrote:
>> >> Justin,
>> >>
>> >> with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2
>> >> rvdw=1.2
>> >> rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp
>> >>
>> >> NOTE 1 [file ./mdps/em.mdp]:
>> >>For energy conservation with switch/shift potentials, rlist should
>> >> be
>> >> 0.1
>> >>to 0.3 nm larger than rvdw.
>> >>
>> >> NOTE 2 [file ./mdps/em.mdp]:
>> >>The sum of the two largest charge group radii (0.078024) is larger
>> >> than
>> >>rlist (1.20) - rvdw (1.20)
>> >>
>> >
>> > As I recall, there is a small bug where grompp ignores rlistlong when
>> > printing
>> > this message.  The simulation will be fine.
>> >
>> > -Justin
>> >
>> >>
>> >> Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same
>> >> value because of PME) ?
>> >>
>> >> 2012/12/7, Justin Lemkul :
>> >>>
>> >>>
>> >>> On 12/7/12 1:19 PM, James Starlight wrote:
>>  Justin,
>> 
>>  following to your advise I've tried to use charmm 27 ff for
>>  simulation
>>  of my protein-cGMP complex ( ligand was parametrized by Swiss Param
>>  server).
>> 
>>  Could you provide me with the cut-offs for vdw as well as
>>  electrostatics suitable for simulation in charmm27 and 36 force
>>  fields?
>> 
>> >>>
>> >>> http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html
>> >>>
>>  Does anybody know another servers for parametrization of the ligands
>>  for charmm simulation in gromacs?
>> 
>> >>>
>> >>> If Google can't find it, it probably doesn't exist.
>> >>>
>> >>> -Justin
>> >>>
>>  2012/12/7, Justin Lemkul :
>> >
>> >
>> > On 12/7/12 11:42 AM, James Starlight wrote:
>> >> Justin,
>> >>
>> >> ligand-only simulation in vacuum have been finished with the same
>> >> errors
>> >> :)
>> >>
>> >> Step 19200, time 38.4 (ps)  LINCS WARNING
>> >> relative constraint deviation after LINCS:
>> >> rms 0.025443, max 0.140660 (between atoms 1 and 3)
>> >> bonds that rotated more than 30 degrees:
>> >> atom 1 atom 2  angle  previous, current, constraint length
>> >>  1  2   52.20.1033   0.0985  0.1000
>> >>  1  3   90.10.1168   0.1141  0.1000
>> >>
>> >> Step 19200, time 38.4 (ps)  LINCS WARNING
>> >> relative constraint deviation after LINCS:
>> >> rms 0.025376, max 0.140474 (between ato

Re: [gmx-users] Re: Pulling ion - US

2012-12-11 Thread Leandro Bortot

 I have made SMD simulations in order to separate a Ca2+ ion from its
complexation site in the protein, which had charge of about -6 e. Without
position constraints  in the protein alpha carbons it unfolded in every
pull simulation.



2012/12/11 Thomas Schlesier 

> wont happen, since the probability that the ion unbounds itself from the
> protein goes down to the cellar. But i hope you get the idea what the
> gerneral problem is. If you the pull-dim in each direction this problem
> wouldn't occur, since the movement of the ion i
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Re: [gmx-users] Is there any tool in gromacs for calculating intermolecular interactions and intramolecular interactions indepedently?

Section 7.4 and chapter 8 of the manual discuss what functionality exists
in the utility tools. If that doesn't help you need to be more specific
about what you mean by "calculate interactions"

Mark

On Tue, Dec 11, 2012 at 2:15 PM, Wu Chaofu  wrote:

> Dear gmxers,
> I am trying to calculate intermolecular interactions and
> intramolecular interactions indepedently. Is there any tool in gromacs
> to do so easily? Could you give me some hints, please? Thanks a lot
> for any replies.
> Chaofu Wu
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Re: [gmx-users] gen-vel=no




On 12/11/12 1:19 AM, Venkat Reddy wrote:

The check point file you submit will have the velocity information.



A checkpoint file is indeed a better set of information to pass to -t, but it is 
not clear if the OP even used -t in the invocation of grompp.  If not, there 
will be a discontinuity in the ensemble and the initial forces are simply 
calculated from the potential of the initial configuration.  This may or may not 
produce stable integration, but at the very least certainly will require some 
time to be discarded as new equilibration.


-Justin



On Tue, Dec 11, 2012 at 10:55 AM, Bahar Mehrpuyan
wrote:


hi gmx user

I've done a production simulation with gen_vel= no, but in grompp I forgot
that use .trr file of equlibration simulation for initial velocities,
my question is how gromacs treats with initial velocities  in this case?

thanks in advance.
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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Atom index (13154) in position_restraints out of bounds




On 12/11/12 1:23 AM, Yun Shi wrote:

Hi all,

I want to restrain the OW of a bound water molecule for the MD of a
protein in water. But the index of this OW is apparently out of range
and I know someone would suggest merging this water with my protein
(e.g. put them in the same .itp file) so as to make them "one
molecule" and thus the index would not be out of bounds.

But I wonder if there is any other way to circumvent this issue?



Position restraints can only be applied per [moleculetype] block, so the global 
numbering cannot be used.  The water molecule you wish to restrain must be 
either (1) in its own block or (2) within another, i.e. the protein.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Atom index (13154) in position_restraints out of bounds

No. Bonded interactions (such as distance restraints) can only be defined
between atoms present in the same [moleculetype]. OTOH a [moleculetype]
doesn't care whether any bonded interactions exist between its atoms or
not, so as long as you obey the constraint that the atom ordering implied
by your [molecules] ordering and ordering of [atoms] within [moleculetypes]
must match that of the coordinate file given to grompp, you're fine. Atom
numbering in the coordinate file to grompp is not important (but you get
told if there's mismatches, IIRC).

Mark

On Tue, Dec 11, 2012 at 7:23 AM, Yun Shi  wrote:

> Hi all,
>
> I want to restrain the OW of a bound water molecule for the MD of a
> protein in water. But the index of this OW is apparently out of range
> and I know someone would suggest merging this water with my protein
> (e.g. put them in the same .itp file) so as to make them "one
> molecule" and thus the index would not be out of bounds.
>
> But I wonder if there is any other way to circumvent this issue?
>
> Thanks,
> Yun
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Re: [gmx-users] Is vacuum simulation NVT?




On 12/11/12 2:09 AM, Jong Wha Lee wrote:

Dear Gromacs users,



Is a vacuum md simulation an NVT simulaton? As the pressure and energy are
not fixed, I think that the only option left is NVT. But without pbc, the
volume would not have been defined. Can it still be called NVT?



In the absence of PBC, you simply have an infinite system.  In a loose sense, 
that may be NVT, but V is infinite, so whether or not you can consider that to 
be constant or not is theoretical math above what I know :)


-Justin

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Department of Biochemistry
Virginia Tech
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Re: [gmx-users] Re: What is the purpose of the [ pairs ] section?

2012-12-11 Thread Bogdan Costescu

Hi Andrew!

I've also been a bit confused by the names when I started looking at
the force field definitions in GROMACS. Although Justin's replies
contain all the information (as usual :)), let's try to shed some
light with an example: consider a chain formed by atoms i-j-k-l-m-n; -
means that there is a bond between atoms.

nrexcl specifies how many neighbors should be excluded when building
lists of nonbonded interactions. nrexcl = 3 means that the first,
second and third order neighbors (j, k and l for atom i; k, l and m
for atom j; l, m and n for atom k; m and n for atom l; n for atom m)
are excluded, such that the following pairs will be put on the lists
to be passed to the nonbonded kernels:

i m
i n
j n

For another force field with nrexcl = 2, the following pairs would be
passed to the nonbonded kernels:

i l
i m
i n
j m
j n
k n

For another force field with nrexcl = 5, no pairs would be passed to
the nonbonded kernels. More generally, any pairs which are neighbors
of higher order than nrexcl will be put on the nonbonded lists.
Parameters for these nonbonded interactions will be automatically
computed from the topology data, based on the combination rules. If
you have empty [bonds], [angles], [dihedrals] and [pairs] sections in
the topology file, only the above interactions are considered for
potential energy calculations. These nonbonded lists are dynamical and
are remade based on neighbor search frequency; when using cutoffs, a
pair whose atoms are further apart than the cutoff is not added to the
list.

Bonded interactions are specified in the [bonds], [angles] and
[dihedrals] sections. Parameters for the bonded interactions are taken
directly from the topology data after matching atom types. Any of
these sections can be empty, if the force field is so designed; for
OPLS-AA all these sections are present. There can be overlaps, f.e. if
nrexcl = 2 and the topology file contains:

[dihedrals]
i j k l
j k l m
k l m n

then atoms i and l, j and m and k and n will interact both as part of
the dihedral angle potential and as nonbonded pair. Some force fields
(like OPLS-AA) specify that the 1-4 interactions ((i l), (j m) and (k
n) in the above example) should indeed be treated both as part of a
dihedral angle potential and as nonbonded pairs; when treating them as
nonbonded pairs there might be a scaling factor (0.5 for OPLS-AA).
When there is no scaling factor (in other words, scaling factor is 1),
a definition like above with nrexcl = 2 is all that is needed. For a
scaling factor different from 1, the GROMACS implementation uses an
explicit pairs list, called [pairs]. All 1-4 interactions should be
included in the [pairs] section, which for the above example would
look like:

[pairs]
i l
j m
k n

It's the user's responsibility to add all needed (1-4 in case of
OPLS-AA) pairs to the [pairs] section; pdb2gmx normally does this, but
if you build the topology through other means then you have to make
sure these pairs are generated. The interactions for these explicit
pairs are always computed - even though they are computed through the
nonbonded kernels, they are not subject to cutoffs. These explicit
pairs also need parameters. The parameters are automatically generated
when gen-pairs = yes from the topology data, based on the combination
rules and the fudge (=scaling) factors. If gen-pairs = no, then the
[pairs] section should contain both the atom indeces and the
parameters. I found the name gen-pairs a bit misleading, I would have
called it gen-pairs-params or something similar as it is only taken
into consideration when looking for parameters; the [pairs] list is
not automatically updated when generating the .tpr file. The [pairs]
section offers some flexibility, as not only the 1-4 interactions but
any other interaction that should be treated the same way can be
included; a possible limitation is that only one fudge factor can be
set for the whole list of explicit pairs.

Care should be taken to not calculate the same interaction twice. With
nrexcl = 3 and:

[pairs]
i m

the nonbonded interaction between atoms i and m will be computed
twice: once as part of explicit pairs list and once as part of
nonbonded lists.

Finally, I would like to point out that most of these can be found by
reading the manual and experimenting with a toy molecular system (like
the example above) using gmxdump and a combination of mdrun -rerun and
g_energy.

Cheers,
Bogdan

On Mon, Dec 10, 2012 at 9:13 PM, Andrew DeYoung  wrote:
> Javier and Mark,
>
> Thank you SO much!  That is so helpful to me.
>
> If you have time, I have two follow-up questions:
>
> (1) From your answer, it seems that in OPLS, 1-4 interactions will be taken
> into account (scaled by fudge) ONLY if the 1-4 atomic indices are specified
> in [ pairs ], even if gen-pairs = yes and sigma and epsilon values are
> provided in [ atomtypes ] in ffnonbonded.itp.
>
> But what about 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions, in a
> protein for example?

Re: [gmx-users] Umbrella sampling - chain A does not get pulled




On 12/11/12 2:40 AM, Davide Mercadante wrote:

Dear Justin,

I have been practicing umbrella sampling simulations following your tutorial
step by step. I have just finished to perform the pull simulations to
identify the configurations to use in the umbrella runs. I have used the
distances.pl script to run iteratively g_dist and the resulting file
(summary_distances.dat) is showing a distance between 2.62nm (for conf0.gro)
and 5.3nm (for conf500.gro). I don't seem to have the values reported in the
tutorial at all (in the tutorial is reported that the COM distance would be
something of an order of magnitude lowerŠ) and I am not sure if something is
gone wrong.



The distances shown in the tutorial are just an illustrative example and don't 
necessarily correspond to anything you might obtain.  A distance of 2.62 nm for 
the initial configuration does not seem right to me though; it should be on the 
order of 0.5 nm, coincident with interpeptide spacing in the beta-sheet.



I have also tried to visualize the trajectories but I am not able to see
chain_A moving away from the rest of the fibril. I have set, at the end of
the topol_Protein_chain_B.itp file, the lines suggested to restrain chain B.

#ifdef POSRES_B
#include "posre_Protein_chain_B.itp"
#endif

I have used all the input files given in the tutorial and the commands/files
extensions suggested.

Can you please help me to understand if I am doing something wrong?



What you're reporting is not consistent - your distances increase over time, but 
then you say peptide A does not move away from the others?  That's not possible. 
 If peptide A doesn't move, then the COM distance should remain relatively 
constant.  Are you loading the right trajectory (i.e., the actual SMD, not a 
previous equilibration or something else)?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] DNA simulation




On 12/11/12 5:22 AM, delara aghaie wrote:

Dear Gromacs users

I want to simulate dobule strand DNA using gromacs. I have read that I should 
use amber forcefield for DNA simulation and I have crossed a web page 
explaining some parameters which I should change in gromacs package to become 
compatible with this amber force filed.



What changes are suggested?  Note that the previous ffamber ports are no longer 
necessary, as native support for AMBER force fields has been present since 
version 4.5.




1) I want to know that is it possible to use straightly pdb2gmx command on pdf 
file of DNA (taken fron protein data bank) and choose amber forcefiled for that?



Yes.


2) Are that changes necessary?



Probably not, but since you haven't said what those changes are, no one can give 
a definitive answer here.




3) If pdb2gmx does not give error how can I make sure about the correctness of 
procedure.


pdb2gmx will read in the parameters from whatever force field you choose.  If it 
succeeds with no errors, then all of those parameters have been applied 
successfully.  Is there some reason you believe there is a problem?


-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields




On 12/11/12 6:04 AM, James Starlight wrote:

Peter, thanks for explanations!


Could you tell me is it possible to convert CGenFF output for
hetatomic group to the RTP   (not an itp ) gromac's data ?

I want to simulate in Gromacs ( in charmm 27 ff) qm\mm GFP protein
which is consist of HETTATOMIC chromophore covently bonded to the
polypeptide chain of that protein so
  I need topology for that chromophore ( I can make it by swiss param
or my CGenFF) but I need that topology in the rtp file format to
integrate it to the aminoacids.rtp  of the Charmm27  for further
processing of the entirely GFP by means of  pdb2gmx.



You've repeated this request several times now, and the answer is always the 
same.  If you have suitable parameters in some form, they need to be converted 
to Gromacs format (.rtp) by some means.  If you haven't found or written some 
program that converts the formats, the only solution is to fire up your favorite 
text editor, open up the Gromacs manual, and get typing.  The .rtp format is 
relatively straightforward, and you will probably be better served if you try to 
write one and post back with specific questions if you have specific problems 
getting it to work.


Note that suitable parameters for the GFP chromophore are published (and that 
paper was linked before in this discussion), so you likely do not need to 
re-derive any of these parameters using SwissParam or CGenFF.  A few years ago, 
we used the published CHARMM27-compatible parameters in a set of GFP simulations.


-Justin


2012/12/8, Peter C. Lai :

On 2012-12-08 03:20:54AM -0800, James Starlight wrote:

1- on what assumptions that blocks were generated ?


This appears to be a swissparm-specific question. I don't know what
algorithms it uses to match what are essentially pharmacophores in the new
molecule with the common individual blocks it finds.


2- Why charge in [ atomtypes ]  (zero) differes from  the charges in


Because gromacs ignores charges in [atomtypes], so the easiest thing is to
just assign all zeros to that column.


the topology of the same groups? how I can check correctness of charge
distribution in such itp files ?


Compare to analogous molecules and see if there are published charges.
You can also use the building blocks and manually assign charges and see
what
you end up with as well. To be totally rigorous, parameterize the structure

using a quantum chemistry package and compare the ab initio charge
distributions to the ones assigned by SwissParm (or by hand).


3- What is sigma andepsilon in the [ atomtypes ] ? :)


LJ interactions in sigma-epsilon form. See gromacs manual section 4.1.1


4- Have anybody else used Swiss param for modeling protein-ligands
systems? Might it be used with the charmm36 set ?



CHARMM has its own generalized forcefield (CGenFF) for ligands and other
molecules, although charmm36 may have cAMP in their nucleotides section...
You can try to also build it using adenine, ribose, and add phosphate.

CGenFF and C36 are interoperable for intermolecular interactions, so if
using CGenFF to paramterize cAMP you would use ParamChem to assign charges
and then convert and add the CGenFF forcefield parameters (from the gromacs
contributions website) to C36. There are mailing list archives that show
you the script to use to do the CGenFF conversion.




James

2012/12/7, Justin Lemkul :



On 12/7/12 2:21 PM, James Starlight wrote:

Justin,

with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2
rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp

NOTE 1 [file ./mdps/em.mdp]:
For energy conservation with switch/shift potentials, rlist should
be
0.1
to 0.3 nm larger than rvdw.

NOTE 2 [file ./mdps/em.mdp]:
The sum of the two largest charge group radii (0.078024) is larger
than
rlist (1.20) - rvdw (1.20)



As I recall, there is a small bug where grompp ignores rlistlong when
printing
this message.  The simulation will be fine.

-Justin



Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same
value because of PME) ?

2012/12/7, Justin Lemkul :



On 12/7/12 1:19 PM, James Starlight wrote:

Justin,

following to your advise I've tried to use charmm 27 ff for
simulation
of my protein-cGMP complex ( ligand was parametrized by Swiss Param
server).

Could you provide me with the cut-offs for vdw as well as
electrostatics suitable for simulation in charmm27 and 36 force
fields?



http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html


Does anybody know another servers for parametrization of the ligands
for charmm simulation in gromacs?



If Google can't find it, it probably doesn't exist.

-Justin


2012/12/7, Justin Lemkul :



On 12/7/12 11:42 AM, James Starlight wrote:

Justin,

ligand-only simulation in vacuum have been finished with the same
errors
:)

Step 19200, time 38.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025443, max 0.140660 (between atom

[gmx-users] Protein-POPC-water

2012-12-11 Thread Shima Arasteh



 Dears,

I am trying to simulate a system of water, POPC and protein using charmm36 ff.
I follow the protocol suggested in KALP15-DPPC tutorial.
I follow the tutorial step by step up to NVT equilibration without any bond or 
any  other type warnings. 
Then I run the grompp :
  # grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

My nvt.mdp file is as :
define        = -DPOSRES   
; Parameters describing the details of the NVT simulation protocol
integrator    = md 
dt        = 0.002      
nsteps        = 5   
; Parameters controlling output writing
nstxout        = 1000       
nstvout        = 1000       
nstenergy    = 1000 
nstlog        = 1000        

; Parameters describing neighbors searching and details about interaction 
calculations
ns_type        = grid 
nstlist        = 5       
rlist        = 1.2       
rlistlong   = 1.4
rcoulomb    = 1.2    
rvdw        = 1.2       
pbc        = xyz        

; Parameters for treating bonded interactions
continuation    = no 
constraint_algorithm = LINCS    
constraints    = all-bonds  
lincs_iter    = 1    
lincs_order    = 4 

; Parameters for treating electrostatic interactions
coulombtype    = PME       
pme_order    = 4 
fourierspacing    = 0.16        

; Temperature coupling parameters
tcoupl        = v-rescale        
tc-grps        = Protein POPC    SOL_CL    ; Define groups to be coupled 
separately to temperature bath
tau_t        = 0.1    0.1    0.1       
ref_t        = 310     310    310       

; Pressure coupling parameters
pcoupl        = no       

; Miscellaneous control parameters
; Dispersion correction
DispCorr    = EnerPres 
; Initial Velocity Generation
gen_vel        = yes      
gen_temp    = 310      
gen_seed    = -1      
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm        = 1           
comm_mode    = Linear        
comm_grps    = Protein_POPC SOL_CL   



  # mdrun -deffnm nvt -v

In this step, the nvt is not done and what I get is as :
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
step 0Warning: 1-4 interaction between 4707 and 4716 at distance 3.491 which is 
larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 23534.929688 (between atoms 257 and 258)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 885865856.00 (between atoms 4521 and 4520)

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 7.158197 (between atoms 3763 and 3765)
   3797   3796   90.0    0.   0.2486  0.
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 11.492531 (between atoms 3712 and 3710)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4472   4469   39.4    0.   0.1029  0.
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4471   4469   89.9    0.   0.1222  0.
    229    231  114.8    0.1756 169.1857  0.1430
    229    230   77.2    0.1053   4.3596  0.0997
   3796   3797   90.0    0.   0.2486  0.
    231    251  118.0    0.1810 161.6257  0.1490
   3777   3775   52.8    0.   0.1136  0.
    231    232  166.9    0.1366 138.9714  0.1080
   3776   3775   89.2    0.   0.1218  0.
    251    252   33.6    0.1300   7.0818  0.123

and finaly some pdb files are printed.
What's the problem? I checked some of atom pairs in this note, however some 
usual bonds are expected.


Sincerely,
Shima
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Re: [gmx-users] Protein-POPC-water




On 12/11/12 8:45 AM, Shima Arasteh wrote:



  Dears,

I am trying to simulate a system of water, POPC and protein using charmm36 ff.
I follow the protocol suggested in KALP15-DPPC tutorial.
I follow the tutorial step by step up to NVT equilibration without any bond or 
any  other type warnings.
Then I run the grompp :
   # grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

My nvt.mdp file is as :
define= -DPOSRES
; Parameters describing the details of the NVT simulation protocol
integrator= md
dt= 0.002
nsteps= 5
; Parameters controlling output writing
nstxout= 1000
nstvout= 1000
nstenergy= 1000
nstlog= 1000

; Parameters describing neighbors searching and details about interaction 
calculations
ns_type= grid
nstlist= 5
rlist= 1.2
rlistlong   = 1.4
rcoulomb= 1.2
rvdw= 1.2
pbc= xyz



Note that you should be using a switch potential for vdW interactions:

http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html


; Parameters for treating bonded interactions
continuation= no
constraint_algorithm = LINCS
constraints= all-bonds
lincs_iter= 1
lincs_order= 4

; Parameters for treating electrostatic interactions
coulombtype= PME
pme_order= 4
fourierspacing= 0.16

; Temperature coupling parameters
tcoupl= v-rescale
tc-grps= Protein POPCSOL_CL; Define groups to be coupled 
separately to temperature bath
tau_t= 0.10.10.1
ref_t= 310 310310

; Pressure coupling parameters
pcoupl= no

; Miscellaneous control parameters
; Dispersion correction
DispCorr= EnerPres
; Initial Velocity Generation
gen_vel= yes
gen_temp= 310
gen_seed= -1
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm= 1
comm_mode= Linear
comm_grps= Protein_POPC SOL_CL



   # mdrun -deffnm nvt -v

In this step, the nvt is not done and what I get is as :
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
step 0Warning: 1-4 interaction between 4707 and 4716 at distance 3.491 which is 
larger than the 1-4 table size 2.200 nm


The fact that NVT fails immediately (i.e. at step zero) indicates that energy 
minimization did not reach a sufficiently low value of Fmax.  You probably have 
unresolved clashes in the system.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] force autocorrelation

2012-12-11 Thread khuws

Hi
Does anyone know if, and if so how, GROMACS can generate a force
autocorrelation function? 
If this is not possible then can I extract the force exterted by each atom
on a single labelled atom?
Regards
Ted



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Re: [gmx-users] GPU warnings

2012-12-11 Thread Szilárd Páll

Hi Thomas,

It looks like some gcc 4.7-s don't work with CUDA, although I've been using
various Ubuntu/Linaro versions, most recently 4.7.2 and had no
issues whatsoever. Some people seem to have bumped into the same problem
(see http://goo.gl/1onBz or http://goo.gl/JEnuk) and the suggested fix is
to put
#undef _GLIBCXX_ATOMIC_BUILTINS
#undef _GLIBCXX_USE_INT128
in a header and pre-include it for nvcc by calling it like this:
nvcc --pre-include undef_atomics_int128.h

Cheers,

--
Szilárd



On Sun, Dec 9, 2012 at 12:18 PM, Thomas Evangelidis wrote:

> > > gcc 4.7.2 is not supported by any CUDA version.
> > >
> >
> > I suggest that you just fix it by editing the include/host_config.h and
> > changing the version check macro (line 82 AFAIK). I've never had real
> > problems with using new and officially not supported gcc-s, the version
> > check is more of a promise from NVIDIA that "we've tested thoroughly
> > internally and we more or less vouch for thins combination".
> >
> > Cheers,
> > --
> > Szilárd
> >
> > PS:
> > Disclamer: I don't take responsibility if your machine goes up in flames!
> > ;)
> >
> >
> Hi Szilárd,,
>
> I tried to compile gromacs-4.6beta1, is this the version you suggested? If
> not, please indicate how to download the source cause I am confused with
> all these development versions.
>
> Anyway, this is the error I get with 4.6beta1, gcc 4.7.2 and cuda 5:
>
> [  0%] Building NVCC (Device) object
>
> src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
>
> /usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(48):
> error: identifier "__atomic_fetch_add" is undefined
>
>
> /usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(52):
> error: identifier "__atomic_fetch_add" is undefined
>
> 2 errors detected in the compilation of
> "/tmp/tmpxft_2394_-9_cudautils.compute_30.cpp1.ii".
> CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:252 (message):
>   Error generating file
>
>
> /home/thomas/Programs/gromacs-4.6-beta1_gnu_cuda5_build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
>
>
> gmake[3]: ***
>
> [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
> Error 1
> gmake[2]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
> Error 2
> gmake[1]: *** [src/programs/mdrun/CMakeFiles/mdrun.dir/rule] Error 2
> gmake: *** [mdrun] Error 2
>
>
> Unless I am missing something, cuda 5 does not support gcc 4.7.2.
>
>
>  Thomas
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Re: [gmx-users] force autocorrelation

1. Run mdrun with nstfout set appropriately
2. g_traj -h
3. g_analyze -h
4. Profit!

Mark

On Tue, Dec 11, 2012 at 3:31 PM, khuws  wrote:

> Hi
> Does anyone know if, and if so how, GROMACS can generate a force
> autocorrelation function?
> If this is not possible then can I extract the force exterted by each atom
> on a single labelled atom?
> Regards
> Ted
>
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/force-autocorrelation-tp5003656.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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[gmx-users] Essential dynamics (ED) sampling using make_edi

2012-12-11 Thread bipin singh

Hello All,

I want to use the essential dynamics (ED) sampling  method to simulate the
unfolding to folding process using make_edi option of GROMACS. For this
task I am using -radcon option (acceptance radius contraction along the
first two eigenvectors towards the folded structure (b4md.gro)) of make_edi
as below:

*make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -tar b4md.gro
-radcon 1-2 -o sam.edi
*
*b4md.gro:* folded structure (C-alpha only)
*topol.tpr: *all atom *
eigenvec.trr*:from g_covar (C-alpha only)

Is this is the correct way of doing the ED sampling...


Also I am not sure about the following:

*1)* How to judge the correct/appropriate value for the:

  -maxedsteps

*2)* How to judge the appropriate values for the following parameters for
an Essential dynamics sampling input *(or it is neglected for ED sampling
and used only for flooding input ) *

-deltaF0
-deltaF
-tau
-alpha
-T

*3) *Will the output trajectory (produced using mdrun -ei sam.edi ) contain
all atoms or only the C-alpha atoms (using the above make_edi command).

-- 
*---
Thanks and Regards,
Bipin Singh*
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Re: [gmx-users] glibc error

We don't yet have enough information to help you. What GROMACS version?
Does it happen under other conditions?

Mark

On Tue, Dec 11, 2012 at 9:06 AM, vahid garshasbi wrote:

> hi
> when I run g_density in X AND Y direction in my program I have this error:
> *** glibc detected *** g_density: munmap_chunk(): invalid pointer:
> 0xb8f863f0 ***
> what is it? what should i do?
>
> thx
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Re: [gmx-users] GPU warnings

2012-12-11 Thread Mirco Wahab


Am 11.12.2012 16:04, schrieb Szilárd Páll:

It looks like some gcc 4.7-s don't work with CUDA, although I've been using
various Ubuntu/Linaro versions, most recently 4.7.2 and had no
issues whatsoever. Some people seem to have bumped into the same problem
(see http://goo.gl/1onBz or http://goo.gl/JEnuk) and the suggested fix is
to put
#undef _GLIBCXX_ATOMIC_BUILTINS
#undef _GLIBCXX_USE_INT128
in a header and pre-include it for nvcc by calling it like this:
nvcc --pre-include undef_atomics_int128.h


The same problem occurs in SuSE 12.2/x64 with it's default 4.7.2
(20120920).

Another possible fix on SuSE 12.2: install the (older) gcc repository
from 12.1/x64 (with lower priority), install the gcc/g++ 4.6 from there
as an alternative compiler and select the "active gcc" through the
"update-alternatives --config gcc" mechanism. This works very well.

Regards

M.

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Re: [gmx-users] GPU warnings

2012-12-11 Thread Szilárd Páll

On Tue, Dec 11, 2012 at 6:49 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:

> Am 11.12.2012 16:04, schrieb Szilárd Páll:
>
>  It looks like some gcc 4.7-s don't work with CUDA, although I've been
>> using
>> various Ubuntu/Linaro versions, most recently 4.7.2 and had no
>> issues whatsoever. Some people seem to have bumped into the same problem
>> (see http://goo.gl/1onBz or http://goo.gl/JEnuk) and the suggested fix is
>> to put
>> #undef _GLIBCXX_ATOMIC_BUILTINS
>> #undef _GLIBCXX_USE_INT128
>> in a header and pre-include it for nvcc by calling it like this:
>> nvcc --pre-include undef_atomics_int128.h
>>
>
> The same problem occurs in SuSE 12.2/x64 with it's default 4.7.2
> (20120920).
>
> Another possible fix on SuSE 12.2: install the (older) gcc repository
> from 12.1/x64 (with lower priority), install the gcc/g++ 4.6 from there
> as an alternative compiler and select the "active gcc" through the
> "update-alternatives --config gcc" mechanism. This works very well.
>

Thanks for the info. The Ubuntu/Linaro version must have a fix for
this. Unfortunately, we can't do much about it and gcc 4.7 is anyway
blocked by the CUDA 5.0 headers.

FYI: Verlet scheme nonbonded kernels (and probably the group scheme as
well), especially with AVX, can be quite a bit slower with older gcc
versions.

I find it really annoying (and stupid) that NVIDIA did not fix their
compiler to work with gcc 4.7 which had already been out for almost a half
a year at the time of the CUDA 5.0 release.

--
Szilárd


>
> Regards
>
> M.
>
>
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[gmx-users] intermolecular rdfs for a bulky cation

2012-12-11 Thread Jeevapani Ha

Hi, 

I need to calculate intermolecular rdfs b/w atoms of P+14,6,6,6 cations on 
gromacs. The cation has three, 6 carbon tails ,  a 14 carbon (long) tail and a 
P at the center. 

I used nrexcl=21 in the .top file.

I believe this job needs a lot memory and the job dies after some time.

1) How can I calculate the intermolecular rdfs for this system?

2) Is my nrexcl value wrong here?


Thanks for your help
Har

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Re: [gmx-users] Is vacuum simulation NVT?

2012-12-11 Thread Michael Shirts

> In the absence of PBC, you simply have an infinite system.  In a loose
> sense, that may be NVT, but V is infinite, so whether or not you can
> consider that to be constant or not is theoretical math above what I know :)

A real molecule in vacuum is usually NVE -- it is not coupled to the
environment, and thus must have conserved energy.  You can certainly
add a thermostat, and then it will be NVT, though it won't be very
much like a real isolated gas molecule.  If you try to run NPT, the
simulation will likely crash because of numerical instabilities, and
there's not much of a point, since you are essentially either 1) in
the ideal gas limit if running with no periodic boundary conditions 2)
in some sort of weird superdilute crystal that really doesn't resemble
anything real if run with a periodic boundary conditions

If you are subtracting out the center of mass motion, then V is not
infinite -- you remove the center of mass degree of freedom, and thus
you have a very different ensemble than if you include the center of
mass motion.  You would need to multiply by V to get the partition
function for an actual gas.

Note that I would strongly suggest sd as the integrator/thermostat,
since there are real issues with ergodicity in systems with only a few
degrees of freedom
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[gmx-users] Re: force autocorrelation

2012-12-11 Thread khuws

Thanks, 
I forgot to mention that I need the force autocorrelation for the forces
acting on a single atom. Will the method

1. Run mdrun with nstfout set appropriately
2. g_traj -h
3. g_analyze -h

 
work here

Keith



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Re: [gmx-users] Re: force autocorrelation

Yes. Read about analysis groups in chapter 8.

Mark

On Tue, Dec 11, 2012 at 8:20 PM, khuws  wrote:

> Thanks,
> I forgot to mention that I need the force autocorrelation for the forces
> acting on a single atom. Will the method
>
> 1. Run mdrun with nstfout set appropriately
> 2. g_traj -h
> 3. g_analyze -h
>
>
> work here
>
> Keith
>
>
>
> --
> View this message in context:
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> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] Re: What is the purpose of the [ pairs ] section?

2012-12-11 Thread Andrew DeYoung

Hi Javier, Mark, Justin, and Bogdan,

Thank you SO much for your time!  The responses that you gave are INCREDIBLY
helpful to me.  I think that they will be very useful, too, to future users
as helpful canonical answers. 

If you have time, I have another question related to the [ pairs ] section.
I generated an .itp file for my large molecule (containing 492 atoms) using
g_x2top, in the OPLS-AA force field.  g_x2top, it seems, specifies all 1-4
interactions in the [ pairs ] section.  

The [ pairs ] section generated by g_x2top for my 492-atom molecule contains
2225 pairs.  I have not checked all 2225 of these pairs (and I should), but
from looking at a subset of them, it appears that these all correctly
correspond to 1-4 interactions, which as Bogdan pointed out, in the OPLS-AA
would be the correct behavior.  (That is, in OPLS-AA, 1-4 interactions --
and only 1-4 interactions -- are specified in [ pairs ], assuming that
nrexcl = 3, which in my case it is.)

Only the indices are specified in my [ pairs ] section, so I have set
gen-pairs = yes to generate (calculate) the parameter combinations, as
Bogdan explained.

But what confuses me is the grompp output, which says:

Generated 276 of the 276 non-bonded parameter combinations 
Generating 1-4 interactions: fudge = 0.5 
Generated 276 of the 276 1-4 parameter combinations

Why is the number of nonbonded interactions 276, and to what does this
refer?  In a previous post in this thread, Justin said that this 276 number
refers only to 1-4 interactions.  If this is the case (and I DO completely
trust Justin!), then why doesn't it say 2225 instead of 276?

Maybe the 276 number refers to the number of UNIQUE combinations found
within the 2225 pairs, but I don't see how this could be since my molecule
only contains four atomtypes (two different carbon atomtypes, one oxygen
atomtype, and one hydrogen atomtype).  Does anyone have any thoughts on
this?

Thank you so much for all of your EXTREMELY helpful explanations, everyone!

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] Re: What is the purpose of the [ pairs ] section?




On 12/11/12 3:36 PM, Andrew DeYoung wrote:

Hi Javier, Mark, Justin, and Bogdan,

Thank you SO much for your time!  The responses that you gave are INCREDIBLY
helpful to me.  I think that they will be very useful, too, to future users
as helpful canonical answers.

If you have time, I have another question related to the [ pairs ] section.
I generated an .itp file for my large molecule (containing 492 atoms) using
g_x2top, in the OPLS-AA force field.  g_x2top, it seems, specifies all 1-4
interactions in the [ pairs ] section.

The [ pairs ] section generated by g_x2top for my 492-atom molecule contains
2225 pairs.  I have not checked all 2225 of these pairs (and I should), but
from looking at a subset of them, it appears that these all correctly
correspond to 1-4 interactions, which as Bogdan pointed out, in the OPLS-AA
would be the correct behavior.  (That is, in OPLS-AA, 1-4 interactions --
and only 1-4 interactions -- are specified in [ pairs ], assuming that
nrexcl = 3, which in my case it is.)

Only the indices are specified in my [ pairs ] section, so I have set
gen-pairs = yes to generate (calculate) the parameter combinations, as
Bogdan explained.

But what confuses me is the grompp output, which says:

Generated 276 of the 276 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 276 of the 276 1-4 parameter combinations

Why is the number of nonbonded interactions 276, and to what does this
refer?  In a previous post in this thread, Justin said that this 276 number
refers only to 1-4 interactions.  If this is the case (and I DO completely
trust Justin!), then why doesn't it say 2225 instead of 276?

Maybe the 276 number refers to the number of UNIQUE combinations found
within the 2225 pairs, but I don't see how this could be since my molecule
only contains four atomtypes (two different carbon atomtypes, one oxygen
atomtype, and one hydrogen atomtype).  Does anyone have any thoughts on
this?



The numbers you get do indeed reflect only unique combinations, if my quick scan 
of the code is correct (grompp is an ugly beast).  It is important to remember 
that the total number of types is not simply those that you have used, but those 
belonging to the parent force field.  grompp will process all of that 
information.  So even if you're only using 4 types for the simulation, I suspect 
that you're actually using a modified version of OPLS-AA that has 23 atom types 
total, a subset of the whole force field.  The full OPLS-AA generates 332520 
combinations, and that's with 800+ atomtypes, even though my protein simulation 
(which reports 332520 combinations being generated) only uses a few dozen atomtypes.


-Justin

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Research Scientist
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Blacksburg, VA
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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Today I've made parametrization of the chromophore group by means of
Swiss param and integrated that topology into charmm27 ff. The only
problem that I have is with the N-term N atom of the chromophore. It's
likely that I made mistake to parametrize it into full protonated form
(NH2).

When I've used pdb2gmx on the GFP structure the peptide bond between
that N atom and adjacent O ( from C term of adjacent residue) is
incorrect ( both oxygens preserves on the C atom so my system had
divided onto 2 chains as well as had incorrect charge). How I could
define the N atom in the topology as the N-terminal? (I've delited
both hydrogens from RTP as well as from HDB files but the problem
didn’t resolved. Also I'm using -ignh on the input pdb to ignore all
hydrogens from the model)

James

2012/12/11, Justin Lemkul :
>
>
> On 12/11/12 6:04 AM, James Starlight wrote:
>> Peter, thanks for explanations!
>>
>>
>> Could you tell me is it possible to convert CGenFF output for
>> hetatomic group to the RTP   (not an itp ) gromac's data ?
>>
>> I want to simulate in Gromacs ( in charmm 27 ff) qm\mm GFP protein
>> which is consist of HETTATOMIC chromophore covently bonded to the
>> polypeptide chain of that protein so
>>   I need topology for that chromophore ( I can make it by swiss param
>> or my CGenFF) but I need that topology in the rtp file format to
>> integrate it to the aminoacids.rtp  of the Charmm27  for further
>> processing of the entirely GFP by means of  pdb2gmx.
>>
>
> You've repeated this request several times now, and the answer is always the
>
> same.  If you have suitable parameters in some form, they need to be
> converted
> to Gromacs format (.rtp) by some means.  If you haven't found or written
> some
> program that converts the formats, the only solution is to fire up your
> favorite
> text editor, open up the Gromacs manual, and get typing.  The .rtp format is
>
> relatively straightforward, and you will probably be better served if you
> try to
> write one and post back with specific questions if you have specific
> problems
> getting it to work.
>
> Note that suitable parameters for the GFP chromophore are published (and
> that
> paper was linked before in this discussion), so you likely do not need to
> re-derive any of these parameters using SwissParam or CGenFF.  A few years
> ago,
> we used the published CHARMM27-compatible parameters in a set of GFP
> simulations.
>
> -Justin
>
>> 2012/12/8, Peter C. Lai :
>>> On 2012-12-08 03:20:54AM -0800, James Starlight wrote:
 1- on what assumptions that blocks were generated ?
>>>
>>> This appears to be a swissparm-specific question. I don't know what
>>> algorithms it uses to match what are essentially pharmacophores in the
>>> new
>>> molecule with the common individual blocks it finds.
>>>
 2- Why charge in [ atomtypes ]  (zero) differes from  the charges in
>>>
>>> Because gromacs ignores charges in [atomtypes], so the easiest thing is
>>> to
>>> just assign all zeros to that column.
>>>
 the topology of the same groups? how I can check correctness of charge
 distribution in such itp files ?
>>>
>>> Compare to analogous molecules and see if there are published charges.
>>> You can also use the building blocks and manually assign charges and see
>>> what
>>> you end up with as well. To be totally rigorous, parameterize the
>>> structure
>>>
>>> using a quantum chemistry package and compare the ab initio charge
>>> distributions to the ones assigned by SwissParm (or by hand).
>>>
 3- What is sigma andepsilon in the [ atomtypes ] ? :)
>>>
>>> LJ interactions in sigma-epsilon form. See gromacs manual section 4.1.1
>>>
 4- Have anybody else used Swiss param for modeling protein-ligands
 systems? Might it be used with the charmm36 set ?

>>>
>>> CHARMM has its own generalized forcefield (CGenFF) for ligands and other
>>> molecules, although charmm36 may have cAMP in their nucleotides
>>> section...
>>> You can try to also build it using adenine, ribose, and add phosphate.
>>>
>>> CGenFF and C36 are interoperable for intermolecular interactions, so if
>>> using CGenFF to paramterize cAMP you would use ParamChem to assign
>>> charges
>>> and then convert and add the CGenFF forcefield parameters (from the
>>> gromacs
>>> contributions website) to C36. There are mailing list archives that show
>>> you the script to use to do the CGenFF conversion.
>>>
>>>
>>>
 James

 2012/12/7, Justin Lemkul :
>
>
> On 12/7/12 2:21 PM, James Starlight wrote:
>> Justin,
>>
>> with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2
>> rvdw=1.2
>> rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp
>>
>> NOTE 1 [file ./mdps/em.mdp]:
>> For energy conservation with switch/shift potentials, rlist
>> should
>> be
>> 0.1
>> to 0.3 nm larger than rvdw.
>>
>> NOTE 2 [file ./mdps/em.mdp]:
>> The sum of the two largest charg

Fw: [gmx-users] intermolecular rdfs for a bulky cation

2012-12-11 Thread Jeevapani Ha


> Hi, 
> 
> I need to calculate intermolecular rdfs b/w 
> P+14,6,6,6 cations.  The cation has three, 6
> carbon tails ,  a 14 carbon (long) tail and a Phosphorous at the
> center. 
> 
> I used nrexcl=21 in the .top file.
> 
> I believe this job needs a lot of memory and the job dies after
> some time.
> 
> 1) How can I calculate the intermolecular rdfs for this
> system?
> 
> 2) Is my nrexcl value wrong here?
> 
> 
> Thanks for your help
> Har
> 
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[gmx-users] Solvating Podophyllotoxin in ethanol

2012-12-11 Thread Hovakim Grabski

Dear Gromacs users,
I've been trying to solvate  Podophyllotoxin in ethanol. I used chimera and 
acpype to create PPT and I got the .itp and .pdb files.
For ethanol I used http://virtualchemistry.org/molecules/64-17-5/index.php .top 
and GAFF liquid structure .pdb file.
Since some atomtypes match between PTOX.itp and ETA.itp, I changed atomtypes in 
PTOX to uppercase and when I try Energy Minimization, I get:


WARNING 1 [file PTOX.itp, line 6]:
  Overriding atomtype OS


WARNING 2 [file PTOX.itp, line 7]:
  Overriding atomtype CA


WARNING 3 [file PTOX.itp, line 8]:
  Overriding atomtype C


WARNING 4 [file PTOX.itp, line 9]:
  Overriding atomtype O


WARNING 5 [file PTOX.itp, line 10]:
  Overriding atomtype OH


WARNING 6 [file PTOX.itp, line 11]:
  Overriding atomtype H1


WARNING 7 [file PTOX.itp, line 12]:
  Overriding atomtype HA


WARNING 8 [file PTOX.itp, line 13]:
  Overriding atomtype HC


WARNING 9 [file PTOX.itp, line 14]:
  Overriding atomtype HO


WARNING 10 [file PTOX.itp, line 15]:
  Overriding atomtype H2

Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations

---
Program grompp, VERSION 4.5.5
Source code file: /home/john1990/code/gromacs-4.5.5/src/kernel/topio.c, line: 
656

Fatal error:
Syntax error - File ETA.itp, line 13
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


This is the order in my topology file:


; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"



;Include PTOX topology
#include "PTOX.itp"


; Include ethanol topology
#include "ETA.itp"

Is there any way to fix it?
Thanks in advance,
Best regards,
Hovakim Grabski
Russian-Armenian(Slavonic) University
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[gmx-users] g_x2top help

2012-12-11 Thread Milinda Samaraweera



Hi Gromacs users

I have a problem Im trying to form a .top file using a g_x2top -f -o -ff 
command. I have defined .n2t .rtp .itp files. and wanted to construct a 
topology file. but the script does not identify any of the atoms from .gro file.

my .n2t file 

; clayff
; n2t
H    h*    0.4100 1.008  1    O  0.100 ;water hydrogen
H    ho    0.4250 1.008  1    O  0.100             ;hydrxyl hydrogen
O    o*   -0.8200    15.998  2    H  0.100    H  0.100 ;water oxygen
O    oh   -0.9500    15.998  1    H  0.100             ;hydroxyl oxygen
O    ob   -1.0500    15.998  0                     ;bridging oxygen
O  obos   -1.1808    15.998  0                     ;bridging oxygen with 
octahedral substitution
O  obts   -1.1688    15.998  0                     ;bridging oxygen with 
tetrahedral substitution
O  obss   -1.2996    15.998  0                     ;bridging oxygen with double 
substitution 
O   ohs   -1.0808    15.998  1      H  0.100       ;hydroxyl hydrogen with 
substitution
Si   st    2.1000    28.086  0                     ;tetrahedral silicon
Al   ao    1.5750    26.982  0                     ;octahedral aluminium
Al   at    1.5750    26.982  0                     ;tetrahedral aluminium
Mg  mgo    1.3600    24.305  0                     ; octahedral magnisium
Na   Na    1.    22.999  0                 ;sodium ion         

my.itp file 

; 
; 

[ defaults ]
; nbfunc    comb-rule   gen-pairs   fudgeLJ fudgeQQ
1   3   yes 0.5 0.5
; parameters are taken from the clay force field

[ atomtypes ]
; The charges here will be overwritten by those in the rtp file
; name   mass  charge    ptype  sigma  eps
  h*   1  1.00800 0.4100    A    0.0e-01  0.0e-01 
;clayFF_waterhydrogen
  ho   1  1.00800 0.4250    A    0.0e-01  0.0e-01 
;clayFF_hydroxylhydrogen
  o*   8 15.99800    -0.8200    A    3.16557e-01  6.50209e-01 
;ClayFF_wateroxygen
  oh   8 15.99800    -0.9500    A    3.16557e-01  6.50209e-01 
;ClayFF_hydroxyloxygen
  ob   8 15.99800    -1.0500    A    3.16557e-01  6.50209e-01 
;ClayFF_bridgingoxygen
  obos 8 15.99800    -1.1808    A    3.16557e-01  6.50209e-01 
;ClayFF_bridgingoxygenoctasub
  obts 8 15.99800    -1.1688    A    3.16557e-01  6.50209e-01 
;ClayFF_bridgingoxygentetrsub
  ohs  8 15.99800    -1.0808    A    3.16557e-01  6.50209e-01 
;ClayFF_hydroxyloxygensub
  st  14 28.08600 2.1000    A    3.30208e-01  8.0e-06        
;ClayFF_tetrahedralsilicon
  ao  13 26.98200 1.5750    A    4.27128e-01  6.0e-06 
;ClayFF_octahedalaluminium
  at  13 26.98200 1.5750    A    3.30206e-01  8.0e-06        
;ClayFF_tetrasubaluminium
  mgo 12 24.30500 1.3600    A    5.26437e-01  4.0e-06        
;ClayFF_octasubmagnisium
  Na  11 22.999   1.    A    1.89744e-01  6.72427e-01    ;ClayFF_Na
                          
[ bondtypes ]
; i    j func    b0  kb
  oh    ho  1    0.1   463711.2         ; O-H
 ohs    ho  1    0.1   463711.2         ; O-H
  o*    h*  1    0.1   463711.2         ; O-H

[ angletypes ]
  ao oh ho  1   109.470    251.046   ; angle Al-O-H
  mgo    ohs    ho  1   109.470    251.046   ; angle Mg-O-H
  h* o* h*  1   109.470    383.009   ; angle H-O-H

[ dihedraltypes ]

my .gro file

1Created by VESTA
 2808
    Clay    ao    1   0.005   0.564  -0.021
    Clay    ao    2  -0.602   0.564   3.099
    Clay    ao    3   4.226   0.564  -0.021
    Clay    ao    4   3.620   0.564   3.099
    Clay    st    5   0.178   0.254   0.256
    Clay    ob    6   0.175   0.240   0.090
    Clay    ob    7   0.201   0.411   0.296
    Clay    ob    8   0.037   0.622   0.318
    Clay    oh    9   0.192  -0.046   0.090
    Clay    oh   10   0.192   3.610   0.090
    Clay    ho   11   0.099  -0.046   0.151
    Clay    ho   12   0.099   3.610   0.151
    Clay    st   13   0.058   0.254   1.263
    Clay    ob   14   0.061   0.240   1.429
    Clay    ob   15   0.035   0.411   1.222
    Clay    ob   16   0.199   0.622   1.200
    Clay    oh   17   0.044  -0.046   1.429
    Clay    oh   18   0.044   3.610   1.429
    Clay    ho   19   0.136  -0.046   1.368
    Clay    ho   20   0.136   3.610   1.368
    Clay    ao   21   0.005   0.259  -0.021
    Clay    ao   22  -0.602   0.259   3.099
    Clay    ao   23   4.226   0.259  -0.021
    Clay    ao   24   3.620   0.259   3.099
    Clay    st   25   0.058   0.568   1.263
    Clay    ob   26   0.061   0.582   1.429
    Clay    ob   27   0.199   0.200   1.200
    Clay    st   28   0.178   0.568   0.256
    Clay    ob   29   0.175   0.582   0.090
    Clay    ob   30   0.037   0.200   0.318
    Clay    ao   31   0.268   0.107  -0.021
    Clay    ao   32  -0.338   0.107   3.099

could any one please let me know what might be the problem

best


Milinda Samaraweera
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 30

[gmx-users] apply force to the protein

2012-12-11 Thread Congyue Wang

Dear all
I want to apply a force to only one direction of the protein to let it go
through a pore, can gromacs meet my needs?
thank you.
-- 
Regards
Congyue Wang
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Re: [gmx-users] apply force to the protein




On 12/11/12 4:55 PM, Congyue Wang wrote:

Dear all
I want to apply a force to only one direction of the protein to let it go
through a pore, can gromacs meet my needs?


Yes.  Read about the pull code in the manual.

-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_x2top help




On 12/11/12 4:40 PM, Milinda Samaraweera wrote:



Hi Gromacs users

I have a problem Im trying to form a .top file using a g_x2top -f -o -ff 
command. I have defined .n2t .rtp .itp files. and wanted to construct a 
topology file. but the script does not identify any of the atoms from .gro file.

my .n2t file

; clayff
; n2t
Hh*0.4100 1.008  1O  0.100 ;water hydrogen
Hho0.4250 1.008  1O  0.100 ;hydrxyl hydrogen
Oo*   -0.820015.998  2H  0.100H  0.100 ;water oxygen
Ooh   -0.950015.998  1H  0.100 ;hydroxyl oxygen
Oob   -1.050015.998  0 ;bridging oxygen
O  obos   -1.180815.998  0 ;bridging oxygen with 
octahedral substitution
O  obts   -1.168815.998  0 ;bridging oxygen with 
tetrahedral substitution
O  obss   -1.299615.998  0 ;bridging oxygen with double 
substitution
O   ohs   -1.080815.998  1  H  0.100   ;hydroxyl hydrogen with 
substitution
Si   st2.100028.086  0 ;tetrahedral silicon
Al   ao1.575026.982  0 ;octahedral aluminium
Al   at1.575026.982  0 ;tetrahedral aluminium
Mg  mgo1.360024.305  0 ; octahedral magnisium
Na   Na1.22.999  0 ;sodium ion

my.itp file

;
;

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   3   yes 0.5 0.5
; parameters are taken from the clay force field

[ atomtypes ]
; The charges here will be overwritten by those in the rtp file
; name   mass  chargeptype  sigma  eps
   h*   1  1.00800 0.4100A0.0e-01  0.0e-01 
;clayFF_waterhydrogen
   ho   1  1.00800 0.4250A0.0e-01  0.0e-01 
;clayFF_hydroxylhydrogen
   o*   8 15.99800-0.8200A3.16557e-01  6.50209e-01 
;ClayFF_wateroxygen
   oh   8 15.99800-0.9500A3.16557e-01  6.50209e-01 
;ClayFF_hydroxyloxygen
   ob   8 15.99800-1.0500A3.16557e-01  6.50209e-01 
;ClayFF_bridgingoxygen
   obos 8 15.99800-1.1808A3.16557e-01  6.50209e-01 
;ClayFF_bridgingoxygenoctasub
   obts 8 15.99800-1.1688A3.16557e-01  6.50209e-01 
;ClayFF_bridgingoxygentetrsub
   ohs  8 15.99800-1.0808A3.16557e-01  6.50209e-01 
;ClayFF_hydroxyloxygensub
   st  14 28.08600 2.1000A3.30208e-01  8.0e-06
;ClayFF_tetrahedralsilicon
   ao  13 26.98200 1.5750A4.27128e-01  6.0e-06 
;ClayFF_octahedalaluminium
   at  13 26.98200 1.5750A3.30206e-01  8.0e-06
;ClayFF_tetrasubaluminium
   mgo 12 24.30500 1.3600A5.26437e-01  4.0e-06
;ClayFF_octasubmagnisium
   Na  11 22.999   1.A1.89744e-01  6.72427e-01;ClayFF_Na

[ bondtypes ]
; ij funcb0  kb
   ohho  10.1   463711.2 ; O-H
  ohsho  10.1   463711.2 ; O-H
   o*h*  10.1   463711.2 ; O-H

[ angletypes ]
   ao oh ho  1   109.470251.046   ; angle Al-O-H
   mgoohsho  1   109.470251.046   ; angle Mg-O-H
   h* o* h*  1   109.470383.009   ; angle H-O-H

[ dihedraltypes ]

my .gro file

1Created by VESTA
  2808
 Clayao1   0.005   0.564  -0.021
 Clayao2  -0.602   0.564   3.099
 Clayao3   4.226   0.564  -0.021
 Clayao4   3.620   0.564   3.099
 Clayst5   0.178   0.254   0.256
 Clayob6   0.175   0.240   0.090
 Clayob7   0.201   0.411   0.296
 Clayob8   0.037   0.622   0.318
 Clayoh9   0.192  -0.046   0.090
 Clayoh   10   0.192   3.610   0.090
 Clayho   11   0.099  -0.046   0.151
 Clayho   12   0.099   3.610   0.151
 Clayst   13   0.058   0.254   1.263
 Clayob   14   0.061   0.240   1.429
 Clayob   15   0.035   0.411   1.222
 Clayob   16   0.199   0.622   1.200
 Clayoh   17   0.044  -0.046   1.429
 Clayoh   18   0.044   3.610   1.429
 Clayho   19   0.136  -0.046   1.368
 Clayho   20   0.136   3.610   1.368
 Clayao   21   0.005   0.259  -0.021
 Clayao   22  -0.602   0.259   3.099
 Clayao   23   4.226   0.259  -0.021
 Clayao   24   3.620   0.259   3.099
 Clayst   25   0.058   0.568   1.263
 Clayob   26   0.061   0.582   1.429
 Clayob   27   0.199   0.200   1.200
 Clayst   28   0.178   0.568   0.256
 Clayob   29   0.175   0.582   0.090
 Clayob   30   0.037   0.200   0.318
 Clayao   31   0.268   0.107  -0.021
 Clayao   32  -0.338   0.107   3.099

could any one please let me know what might be the problem



Well what error do you get?  There are

Re: [gmx-users] Solvating Podophyllotoxin in ethanol




On 12/11/12 4:30 PM, Hovakim Grabski wrote:

Dear Gromacs users,
I've been trying to solvate  Podophyllotoxin in ethanol. I used chimera and 
acpype to create PPT and I got the .itp and .pdb files.
For ethanol I used http://virtualchemistry.org/molecules/64-17-5/index.php .top 
and GAFF liquid structure .pdb file.
Since some atomtypes match between PTOX.itp and ETA.itp, I changed atomtypes in 
PTOX to uppercase and when I try Energy Minimization, I get:



Atomtypes are case-sensitive, so "OS" and "os" are not, in fact, the same atom 
type.



WARNING 1 [file PTOX.itp, line 6]:
   Overriding atomtype OS


WARNING 2 [file PTOX.itp, line 7]:
   Overriding atomtype CA


WARNING 3 [file PTOX.itp, line 8]:
   Overriding atomtype C


WARNING 4 [file PTOX.itp, line 9]:
   Overriding atomtype O


WARNING 5 [file PTOX.itp, line 10]:
   Overriding atomtype OH


WARNING 6 [file PTOX.itp, line 11]:
   Overriding atomtype H1


WARNING 7 [file PTOX.itp, line 12]:
   Overriding atomtype HA


WARNING 8 [file PTOX.itp, line 13]:
   Overriding atomtype HC


WARNING 9 [file PTOX.itp, line 14]:
   Overriding atomtype HO


WARNING 10 [file PTOX.itp, line 15]:
   Overriding atomtype H2

Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations

---
Program grompp, VERSION 4.5.5
Source code file: /home/john1990/code/gromacs-4.5.5/src/kernel/topio.c, line: 
656

Fatal error:
Syntax error - File ETA.itp, line 13
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


This is the order in my topology file:


; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"



;Include PTOX topology
#include "PTOX.itp"


; Include ethanol topology
#include "ETA.itp"

Is there any way to fix it?


Yes, but you'll need to post the contents of the .itp files if you want 
feedback.  Chapter 5 of the manual explains the required order.  Force-field 
level directives ([defaults], [atomtypes], etc) need to precede the declaration 
of any [moleculetype] block.  From the above fatal error, you are not satisfying 
this requirement.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields




On 12/11/12 4:13 PM, James Starlight wrote:

Today I've made parametrization of the chromophore group by means of
Swiss param and integrated that topology into charmm27 ff. The only
problem that I have is with the N-term N atom of the chromophore. It's
likely that I made mistake to parametrize it into full protonated form
(NH2).



Protonation states of termini can indeed cause problems.  Model compounds often 
use capping groups (methyl, acetyl, etc) to mitigate these effects.  You can 
probably get some tips from http://pubs.acs.org/doi/abs/10.1021/jp014476w, or 
otherwise just use their parameters.



When I've used pdb2gmx on the GFP structure the peptide bond between
that N atom and adjacent O ( from C term of adjacent residue) is
incorrect ( both oxygens preserves on the C atom so my system had
divided onto 2 chains as well as had incorrect charge). How I could
define the N atom in the topology as the N-terminal? (I've delited
both hydrogens from RTP as well as from HDB files but the problem
didn’t resolved. Also I'm using -ignh on the input pdb to ignore all
hydrogens from the model)



Copying and pasting your .rtp and .hdb entries would help.  Also note that the 
chromophore needs to be defined as protein in residuetypes.dat, otherwise the 
protein chain will terminate erroneously and you'll get protonation state problems.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] pbs not returning gromacs files

2012-12-11 Thread John Doe


I'm not sure if this is the right place to be asking this but I haven't been 
able to find an answer.

I'm using a pbs script to submit a parallel job of the water tutorial.  So in 
my home file I have all of the files from the water tutorial and the output 
from grompp.  If I submit my simulation on the head node:
mdrun

then I get all of the output files such as the trajectory.  However, when I try 
to mpiexec with the pbs script I get nothing except stdout.  My pbs script is 
this:

#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=12,mem=10GB:comp
#PBS -N Gromacs_HelloWorld
#PBS -o stdout
#PBS -j oe

module load gromacs-4.5.5
module load openmpi-intel

pbsdcp -s $PBS_O_WORKDIR/* $TMPDIR

cd $TMPDIR

NPROCS=`wc -l < $PBS_NODEFILE`

mpiexec -np $NPROCS mdrun_mpi_d

pbsdcp -g -r '*' $PBS_O_WORKDIR
cd $PBS_O_WORKDIR

this is submitted like:

qsub job.pbs

This runs under 2 seconds and all the output I get is the "stdout".  Any help 
would be greatly appreciated.  
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Re: [gmx-users] g_x2top help



Please keep the discussion on the gmx-users mailing list.

On 12/11/12 5:12 PM, Milinda Samaraweera wrote:

Hi Justin

error is

Could only find a forcefield type for 0 out of 2808 atoms

I attached my input files, and I checked .gro for errors. cant find any



I don't exactly know what you've checked, but I think the problem is what I 
suggested before - your .gro file specifies atom types instead of valid names. 
Your .n2t file cannot match anything.


-Justin


best
Milinda Samaraweera
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA

*From:* Justin Lemkul 
*To:* Milinda Samaraweera ; Discussion list for GROMACS
users 
*Sent:* Tuesday, December 11, 2012 4:59 PM
*Subject:* Re: [gmx-users] g_x2top help



On 12/11/12 4:40 PM, Milinda Samaraweera wrote:
 >
 >
 > Hi Gromacs users
 >
 > I have a problem Im trying to form a .top file using a g_x2top -f -o -ff
command. I have defined .n2t .rtp .itp files. and wanted to construct a topology
file. but the script does not identify any of the atoms from .gro file.
 >
 > my .n2t file
 >
 > ; clayff
 > ; n2t
 > Hh*0.41001.008  1O  0.100;water hydrogen
 > Hho0.42501.008  1O  0.100;hydrxyl hydrogen
 > Oo*  -0.820015.998  2H  0.100H  0.100 ;water oxygen
 > Ooh  -0.950015.998  1H  0.100   ;hydroxyl oxygen
 > Oob  -1.050015.998  0;bridging oxygen
 > O  obos  -1.180815.998  0;bridging oxygen with
octahedral substitution
 > O  obts  -1.168815.998  0;bridging oxygen with
tetrahedral substitution
 > O  obss  -1.299615.998  0;bridging oxygen with double
substitution
 > O  ohs  -1.080815.998  1  H  0.100  ;hydroxyl hydrogen with
substitution
 > Si  st2.1000 28.086  0;tetrahedral silicon
 > Al  ao1.575026.982  0;octahedral aluminium
 > Al  at1.575026.982  0;tetrahedral aluminium
 > Mg  mgo1.360024.305  0; octahedral magnisium
 > Na  Na1.22.999  0;sodium ion
 >
 > my.itp file
 >
 > ;
 > ;
 >
 > [ defaults ]
 > ; nbfunccomb-rule  gen-pairs  fudgeLJ fudgeQQ
 > 1 3  yes0.50.5
 > ; parameters are taken from the clay force field
 >
 > [ atomtypes ]
 > ; The charges here will be overwritten by those in the rtp file
 > ; name  mass  chargeptype  sigma  eps
 >h*  1  1.008000.4100A0.0e-01  0.0e-01
;clayFF_waterhydrogen
 >ho  1  1.008000.4250A0.0e-01  0.0e-01
;clayFF_hydroxylhydrogen
 >o*  815.99800-0.8200A3.16557e-01  6.50209e-01
;ClayFF_wateroxygen
 > oh  815.99800-0.9500A3.16557e-01  6.50209e-01
;ClayFF_hydroxyloxygen
 >ob  815.99800-1.0500A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxygen
 >obos 815.99800-1.1808A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxygenoctasub
 >obts 815.99800-1.1688A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxygentetrsub
 >ohs  815.99800-1.0808A3.16557e-01  6.50209e-01
;ClayFF_hydroxyloxygensub
 >st  1428.086002.1000A3.30208e-01  8.0e-06
;ClayFF_tetrahedralsilicon
 >ao  1326.982001.5750A4.27128e-01  6.0e-06
;ClayFF_octahedalaluminium
 >at  1326.982001.5750A3.30206e-01  8.0e-06
;ClayFF_tetrasubaluminium
 >mgo 1224.305001.3600A5.26437e-01  4.0e-06
;ClayFF_octasubmagnisium
 >Na  1122.999  1.A1.89744e-01  6.72427e-01
;ClayFF_Na
 >
 > [ bondtypes ]
 > ; ij funcb0  kb
 >ohho  10.1  463711.2 ; O-H
 >  ohsho  10.1  463711.2; O-H
 >o*h*  10.1  463711.2; O-H
 >
 > [ angletypes ]
 >aoohho  1  109.470251.046  ; angle Al-O-H
 >mgoohsho  1  109.470251.046  ; angle Mg-O-H
 >h*o*h*  1  109.470383.009  ; angle H-O-H
 >
 > [ dihedraltypes ]
 >
 > my .gro file
 >
 > 1Created by VESTA
 >  2808
 >  Clayao1  0.005  0.564  -0.021
 >   Clayao2  -0.602  0.564  3.099
 >  Clayao3  4.226  0.564  -0.021
 >  Clayao4  3.620  0.564  3.099
 >  Clayst5  0.178  0.254  0.256
 >  Clayob6  0.175  0.240  0.090
 >  Clayob7  0.201  0.411  0.296
 >  Clayob8  0.037  0.622  0.318
 >  Clayoh9  0.192  -0.046  0.090
 >  Clayoh  10  0.192  3.610  0.090
 >  Clayho  11 0.099  -0.046  0.151
 >  Clayho  12  0.099  3.610  0.151
 >  Clayst  13  0.058  0.254  1.263
 >  Clayob  14  0.061  0.240  1.429
 >  Cl

Re: [gmx-users] pbs not returning gromacs files




On 12/11/12 5:10 PM, John Doe wrote:


I'm not sure if this is the right place to be asking this but I haven't been 
able to find an answer.

I'm using a pbs script to submit a parallel job of the water tutorial.  So in 
my home file I have all of the files from the water tutorial and the output 
from grompp.  If I submit my simulation on the head node:
 mdrun

then I get all of the output files such as the trajectory.  However, when I try 
to mpiexec with the pbs script I get nothing except stdout.  My pbs script is 
this:

 #PBS -l walltime=1:00:00
 #PBS -l nodes=1:ppn=12,mem=10GB:comp
 #PBS -N Gromacs_HelloWorld
 #PBS -o stdout
 #PBS -j oe

 module load gromacs-4.5.5
 module load openmpi-intel

 pbsdcp -s $PBS_O_WORKDIR/* $TMPDIR

 cd $TMPDIR

 NPROCS=`wc -l < $PBS_NODEFILE`

 mpiexec -np $NPROCS mdrun_mpi_d

 pbsdcp -g -r '*' $PBS_O_WORKDIR
 cd $PBS_O_WORKDIR

this is submitted like:

 qsub job.pbs

This runs under 2 seconds and all the output I get is the "stdout".  Any help 
would be greatly appreciated.


Is there anything in this file?  Any useful error messages?  If you add 'echo 
$PATH' to your job script, does it correctly find the location of the Gromacs 
executables?


Hopefully your sysadmins would be able to help troubleshoot, within the context 
of any specifics of your cluster.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_densmap: adsorbed species and output format

2012-12-11 Thread anouri

Dear Gromacs users,

I am writing to ask about g_densmap command:

If there are species adsorbed (stagnant) or structured around a frozen
group, for which I want to obtain the density distribution map, g_densmap
calculates unrealistically high densities. (like 2000 /nm3 of water...).
So in visualization, the regions with descent density (like ~ 30 /nm3 for
bulk water) will be shown with the same color code as zero density (because
.xpm supports only 16 colors). I was wondering if there was a way to obtain
the numerical density values (in a 2d matrix) as the output of g_densmap,
rather than the .xpm format.

(One solution is to impose the maximum with an educated guess for -dmax
option, but having the actual numbers would be nicer.)

Furthermore, I was wondering if there is readily a code available to convert
the .xpm image to a matrix with numerical values, if I want to do a
calculation on the density map. Currently I convert the .xpm file to .png,
then import it to MATLAB and use the image processing toolbox to analyze. I
believe this introduces some error to the calculation.

I look forward to receiving your advice!
Thank you,

Amin

--
Amin Nouri
MSc student
Chemistry department, Simon Fraser University

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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields