date:20111118

Hello,

I ve a query.I ve not created .rtp file,.atp file.I ve only .pdb file and
i used pdb2gmx command and successfully got .top,.itp and .gro file.

Do my files contains error without making use of .rtp and .atp files.Its
just a curiosity to know.And how to make .rtp and .atp files.

thanx.


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[gmx-users] difference in forcefields.

2011-11-18 Thread swati patel

Hello Users,

I am facing a problem in obtaining topologies for my ligand.I tried working
on acpype,bt it seems very complex to me.PRODRG is easy but it uses
gromos87 force field.PRODRG 2.5 is still not available for download.

can anyone suggest me how to obtain topologies for my protein and ligand
using same force fields?

thanks.
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[gmx-users] Estimation of free energy using Linear Response method

2011-11-18 Thread Vasileios Tatsis

Dear Gromacs Users,

I would like to ask how the Linear Response method can be applied for the 
calculation of free energy using the Gromacs package?
More specifically, I am interested in the set-up of the MD protocol and the 
parameters of the input files.


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[gmx-users] The time correlation functions for the orientation of the C-H

2011-11-18 Thread intra\sa175950

Hi GMX users, 

 

I am interesting to compute the tcf of C-H bonds for several surfactants in
micelles. Is there a tool in GROMACS to do that ? 

 

Stephane

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Re: [gmx-users] PRODRG2.5 server not found.




swati patel wrote:

Helo Justin,

The link for prodrg 2.5 server is i.e. 
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta is 404 not 
found.How should I proceed further?




http://davapc1.bioch.dundee.ac.uk/prodrg/

-Justin

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Re: [gmx-users] .rtp file




ibi2010...@iiita.ac.in wrote:

Hello,

I ve a query.I ve not created .rtp file,.atp file.I ve only .pdb file and
i used pdb2gmx command and successfully got .top,.itp and .gro file.

Do my files contains error without making use of .rtp and .atp files.Its
just a curiosity to know.And how to make .rtp and .atp files.



The only reason you would need to create or modify existing .rtp and .atp files 
is if you are adding or modifying a new residue to it.  Most standard residues 
are present in the force fields packaged with Gromacs.


If you don't get an error message, there probably weren't any errors :)

-Justin

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Department of Biochemistry
Virginia Tech
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[gmx-users] PRODRG server

2011-11-18 Thread swati patel

Hello Justin,

Sorry for again and again bothering you.But in prodrg2.5 server,there is no
option to choose force fields.It automatically generates topology in gromos
87 force fields.

I am using 4.5 version of gromacs in which gromos force fields are gromos
96.How to match my protein and ligand topologies??

Thanx.
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Re: [gmx-users] PRODRG server




swati patel wrote:

Hello Justin,

Sorry for again and again bothering you.But in prodrg2.5 server,there is 
no option to choose force fields.It automatically generates topology in 
gromos 87 force fields.




The default force field used by the latest PRODRG is Gromos96 43a1, not 
Gromos87.

-Justin

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Department of Biochemistry
Virginia Tech
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[gmx-users] (no subject)

Hello,

I got all confused.So i started with the beginnning.i generated topology
for my protein Streptavidin and generated topology for my ligand using
prodrg2.5 server.

I am getting error at step editconf i.e.Fatal error:Something is wrong in
the coordinate formatting of file conf.gro.

Any suggestions??I made necessary changes to topol.top and conf.gro to
merge ligand topology.

Thanx


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Re: [gmx-users] Gromacs 3D maps


On 18/11/2011 12:24 AM, Alex wrote:

Dear all,

I'd like to transform an md gromacs trajectory in a 3d maps set.
I mean that every 100ps, I need to export frame coordinates to a 3d map.
Than I need to compare a map with the following.
Could give me any advice about tools/software to use?


I don't know what you mean by a 3d map.


Additionally I need to export the coordinate (x,y,z) of atom's protein, deriving
from MD trajectory, to a matrix where each columns are frame number, 1-n
atoms'positions (x,y,z coordinates).
Any suggestion?



Check out manual section 7.4 for clues on what the tools do, then the 
appropriate appendix section for more details. g_traj sounds like a good 
place to start.


Mark
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Re: [gmx-users] (no subject)




ibi2010...@iiita.ac.in wrote:

Hello,

I got all confused.So i started with the beginnning.i generated topology
for my protein Streptavidin and generated topology for my ligand using
prodrg2.5 server.

I am getting error at step editconf i.e.Fatal error:Something is wrong in
the coordinate formatting of file conf.gro.

Any suggestions??I made necessary changes to topol.top and conf.gro to
merge ligand topology.



Something you did was wrong, but it's hard to say.  The problem is with the 
coordinate file, so when you merged the protein and ligand, you broke the format 
somehow.  There are many potential problems.  Please work through the 
protein-ligand tutorial for a guide on how to properly deal with such systems.


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html

-Justin

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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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Re: [gmx-users] problem obtaining similar force fields for protein and ligand


On 18/11/2011 6:54 PM, swati patel wrote:

Hello Users,

I am facing a problem in obtaining topologies for my ligand.I tried 
working on acpype,bt it seems very complex to me.PRODRG is easy but it 
uses gromos87 force field.PRODRG 2.5 is still not available for download.


can anyone suggest me how to obtain topologies for my protein and 
ligand using same force fields?


Suggestions can be found here - 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation


Mark
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Re: [gmx-users] analysing helix dynamics


On 18/11/2011 1:54 PM, jayant james wrote:

Hi all,
During MD simulations of a protein,I find that there are two helices
switch periodically from being parallel and perpendicular to each
other.  I'd like to plot out the orientation of these two helices with
respect to each other, is there a command to extract this information?



Check out the options in 7.4 of the manual and see where they lead you.

Mark
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Re: [gmx-users] non-specific protein-protein interactions


On 18/11/2011 8:10 AM, Ben Reynwar wrote:

Dear gromacs list,

Does anyone know how well current force fields capture the energetics
of non-specific protein-protein interactions?  I'm simulating a
protein with an arm that alternates between (apparently) non-specific
adsorption to the main-body of the protein and free movement in the
solvent.  Can I place any trust in the results of an MD simulation for
something like this?  I haven't seen any comparison of experimental
results with simulation results of the energetics of non-specific
protein-protein interactions so I'm a little skeptical about it.
Currently I'm using generalized born implicit solvent, which is
perhaps a mistake when solvation energies could be critical to the
results.



I'd be very skeptical unless you can observe many adsorption/desorption 
processes and with explicit solvent (though they're probably mutually 
exclusive).


Mark
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Re: [gmx-users] query for energy minimization in solvent


On 18/11/2011 7:40 AM, Anushree Tripathi wrote:
Yes I m using 4.0.7 version.so for that how could I change the name 
accordingly.


You used it in your [molecules] section. Change it to what it should be, 
per ions.itp.


Mark



On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul > wrote:




Anushree Tripathi wrote:

when i run the given command i.e,

grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
It is showing fatal error:No such molecule type NA.
How could I troubleshoot this problem?


Ion naming is listed in ions.itp - the "NA" name works for all
force fields in the Gromacs 4.5.x series.  Older versions had
force field-specific naming so you will have to change the name
accordingly if you're using one of these versions.

-Justin

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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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Re: [gmx-users] what's the math algorithm?


On 18/11/2011 7:29 AM, Liu, Liang wrote:

Dear all,

Assuming I have a some tabulated potentials, table.xvg, tablep.xvg, 
table_P_P.xvg, table_P_C.xvg and so on.
Also there are non-zero values in the first column of both table.xvg 
and tablep.xvg; while the first column (x), the six column (h(x)) and 
the last column (h'(x)) have non-zero numbers.

All other columns have only 0. So what's the math behind it? Thanks.


I think I've referred you to the manual sections on tabulated potentials 
a couple of times. If I haven't, I have now :-)


Mark
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[gmx-users] fatal error occuring.

Hello Justin,

After setting up grompp command,i am getting an error "Atoms in the .top
are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr =
1179)".I am heading up step by step taking your aid.

What should i do?How to correct it??

Thanx.



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Re: [gmx-users] Hydrogen database


On 18/11/2011 3:11 AM, Ehud Schreiber wrote:


Hi,

I have recently studied the hydrogen database format of .hdb files 
(page 118, section 5.6.4 in the manual version 4.5.4). I would like to 
make a few remarks that, if correct, may need addressing.


1)Method 3 of adding the hydrogens, that of two planar hydrogens, 
gives -NH2 as the example. I think this is misleading, as although 
this is true for an amide group --C(=O)NH2 such as in an asparagine 
and glutamine side chains, the nitrogen is tetrahedral in the R-NH2 
case or in the amino acid N-terminus.




True, though attempting to model pyramidal inversion with the usual MM 
tool kit sounds like a recipe for trouble anyway.


A better example for two planar hydrogens would be =CH2 such as in 
ethylene or vinyls.




True, I'll add that to the manual ahead of amide -NH2.

2)The provided methods for adding hydrogens are not covering the whole 
set of possibilities. In particular, it seems to me that three methods 
are lacking, although admittedly they are less common:


a.One tetrahedral hydrogen connected to atom i which is in turn 
connected to two atoms j,k such that n is on the plane bisecting angle 
j-i-k; n-i-j = n-i-k = 109.47 degrees; and dihedral n-i-j-l > 90 
degrees. Example: secondary amines R2NH. This case can be mimicked by 
method 2 with i,j,l atoms so is perhaps superfluous.


b.One planar hydrogen connected to atom i which is connected to only 
one other atom j such that n-i-j = 120 degrees and n-i-j-k is trans. 
Example: R2C=NH.




Yeah I'd use method 2 for both of these and rely on EM to fix it, but 
some hints are in order.


c.One linear hydrogen such that n-i-j is a straight line. Example: #CH 
where # is a triple bond.




That's a potentially useful feature, but method 2 would still be 
acceptable with due care.


3)I haven't checked this, but can the k atom be a hydrogen added in an 
earlier line of the same .hdb file?




I would think so.

Mark
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[gmx-users] Issue in membrane simulation How To

2011-11-18 Thread Gianluca Santoni


Hi all,
I was checking the how to on membrane proteins, and i think there is a 
little error in the section

"Increasing the size of the water segment in the z-direction"

The line
# |cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro|
following the notation of the tutorial, recreates the original .gro 
file, with all the water molecule.

I think it should be replaced by

# |cat not_last_line.gro keep_these_waters.gro last_line.gro > new_system.gro|

I'm also not sure about the line just before, but I'm looking for a way 
to fix it. In any case, it doesn't seem to do its job properly.


Ciao!

--
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Institut de Biologie Structurale
41 rue Horowitz
Grenoble
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Re: [gmx-users] fatal error occuring.




ibi2010...@iiita.ac.in wrote:

Hello Justin,

After setting up grompp command,i am getting an error "Atoms in the .top
are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr =
1179)".I am heading up step by step taking your aid.

What should i do?How to correct it??



Without seeing the topology, it is hard to say exactly what the problem is, but 
the [atoms] section of each [moleculetype] must be (as the error says), numbered 
consecutively, starting with 1.  In at least one instance, these criteria have 
not been met.  Note that in the topology, atom numbering is unique to each 
[moleculetype] - that is, the atom numbering in the .gro has no bearing on the 
numbering in the .top.


-Justin

--


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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] fatal error occuring.

2011-11-18 Thread swati patel

Hello Justin,

Somehow I obtained ligand and protein topology in charmm force fields.

After command grompp,I am getting an error "No such moleculetype LIG" where
lig is my ligand abbreviation.

Any suggestions for my error??

Thanx.
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Re: [gmx-users] fatal error occuring.




swati patel wrote:

Hello Justin,

Somehow I obtained ligand and protein topology in charmm force fields.

After command grompp,I am getting an error "No such moleculetype LIG" 
where lig is my ligand abbreviation.


Any suggestions for my error??


Have you done the proper tutorial material?  The is one for protein-ligand 
complexes that will show you how to set up the topology and coordinate files 
appropriately.  I posted the link earlier today; it is also available on the 
Gromacs website on the Tutorials page.


-Justin

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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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[gmx-users] Extract van der waals surface atoms coordinates

2011-11-18 Thread Alex Jemulin

Dear All
 
How can I extract van der waals surface atoms coordinates from MD Trajectory 
and write them to a file?
Is it possible with gromacs? And with other tools?
Any suggestion?
 
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Re: [gmx-users] Extract van der waals surface atoms coordinates




Alex Jemulin wrote:

Dear All
 
How can I extract van der waals surface atoms coordinates from MD 
Trajectory and write them to a file?

Is it possible with gromacs? And with other tools?


g_sas -i produces a topology of surface atoms, from which you can get atom 
numbers, create an index file, then use g_traj to extract the coordinates of 
those atoms.


-Justin

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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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Re: [gmx-users] Poor exchange probability for REMD


On 18/11/2011 12:43 PM, ÏéÇ« ¿× wrote:

Dear GMX users，
Recently i am performing the REMD simulation with Gromacs program and the temperature 
distribution for each replica was predicted with the server 
"http://folding.bmc.uu.se/remd/";. However, after a 2-ns short test simulation 
with 64 replicas  , i checked the exchange probability for the neighboring replicas and 
find the exchange probability was about 0.3 to 0.4 (as the file i attached )but the 
desired probability was 0.2. Meanwhile, i found the exchange probabilities fluctuated 
markedly for each pair of  replicas while ideally we may hope they were consistent with 
each other.  I don't know whether this is acceptable or must be fixed up, or  a longer 
simulation time and pre-equilibrium at different replica temperature for each replica was 
needed.


Pre-equilibration at the right temperature is always a good idea, not 
just for REMD. However for NVT REMD you need to equilibrate the other 
temperatures at the same box size that is sound for the temperature at 
which you want to make observations.


Even given that, there is no strong reason to suppose that a temperature 
distribution following a simple mathematical formula should lead to 
equal exchange probabilities on a "real" system with free energy 
bottlenecks. Knowing that one might need to be adding more replicas at 
relevant temperatures is something that can only be determined 
empirically - and probably from more than 2ns.


Mark


 The system i simulated  includes 60074 atoms which consists of 155 
residues,19173 waters and 14 chloridions. I first equilibrium the system for 
2ns with NPT ensemble at 300K, then start the REMD simulation for 64 different 
replicas (temperature ranges from 300 to 386K) with NVT ensemble and the 
exchange attempt time was 2-ps(1000 integral steps).
 Now i was totally puzzled and don't know how to figure out these 
problems,i am eager for the help from you and any suggestions will be greatly 
appreciated!
 Best regards!
 Xiangqian Kong


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[gmx-users] g_lie question

2011-11-18 Thread EGY

I am trying to figure out how to use the g_lie tool in gromacs. I have the 
dGbind value for the ligand-solvent interactions and for the protein-ligand 
complex.
However, I cannot find in the manual what units these values are. I get the 
following:
DGbind = 1953867.080 (0.664)
and 
DGbind = 185147.449 (nan)

What does the parentheses mean and what is (nan)? And, what units are these in?

Any input would be greatly appreciated.
Thanks!
2egy--
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Re: [gmx-users] GROMACS/ORCA QMMM

2011-11-18 Thread Jose Tusell

Hi Justin,

I tried using a larger step size but my system blew up...  My guess is
that I have a bad starting structure, I'll work on the initial
structure for the QM region (energy minimize).

When I'm running ORCA I want to have a LJ file to correct for the
interaction of my QM system with the protein.  However this file is
not created when I run QMMM, I've used the bOpt = true in the mdp
file.  Can anyone please offer some help on how to create this LJ
files?

Thanks,

Jose Tusell

On Thu, Nov 17, 2011 at 2:07 PM, swati patel  wrote:
> hello,
> I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated
> Ligand topology from a sofware PRODRG using gromos87 force fields.After
> solvating it,I am getting an error using grompp command
>
> Fatal error:
> Atomtype HW not found
>
> can anyone provide me some help?
>
> Thanx with anticipation.
>
>
> On Fri, Nov 18, 2011 at 2:29 AM, Jose Tusell  wrote:
>>
>> I'll try changing the step size first and if that fails I'll try
>> another algorithm.  Thanks for the input.
>>
>> Jose Tusell
>>
>> On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul 
>> wrote:
>> >
>> >
>> > Jose Tusell wrote:
>> >>
>> >> Hi Justin,
>> >>
>> >> Thanks for the input on why this is happening.   It sounds a little
>> >> suspicious that the energy doesn't change after a few steps of energy
>> >> minimization.  Do you know of any way that I can find out what is
>> >> going on?
>> >>
>> >
>> > The screen output should indicate the atom with maximal force.
>> >  Sometimes
>> > the EM algorithms get stuck when the geometry cannot change without
>> > making
>> > detrimental moves.  You either need a larger step size, a different
>> > algorithm, or a better starting structure, if that is the case.  I have
>> > seen
>> > this many times before, nothing suspicious about it.
>> >
>> > -Justin
>> >
>> >> Thanks,
>> >>
>> >> Jose Tusell
>> >>
>> >> On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul 
>> >> wrote:
>> >>>
>> >>> Jose Tusell wrote:
>> 
>>  Hi Cristoph,
>> 
>>  Thanks for the reply.  I found that my problem was not gromacs.  The
>>  input that ORCA was receiving from GROMACS did not have the correct
>>  number of hydrogens.  I've solved this problem now and ORCA is
>>  running
>>  fine.  I however ran into another problem with my energy
>>  minimization.
>>   The output from my gromacs log file is the following:
>> 
>>           Step           Time         Lambda
>>              0        0.0        0.0
>> 
>>   Energies (kJ/mol)
>>           Bond          Angle    Proper Dih.  Improper Dih.
>>   LJ-14
>>    1.21899e+04    1.92496e+03    5.62567e+03    1.49141e+01
>>   3.68001e+03
>>     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum
>>  En.
>>    2.41200e+04    1.47494e+05   -5.06544e+05   -7.56009e+04
>>  -3.96508e+06
>>      Potential Pressure (bar)
>>   -4.35218e+06   -2.10629e+04
>> 
>>           Step           Time         Lambda
>>              1        1.0        0.0
>> 
>>   Energies (kJ/mol)
>>           Bond          Angle    Proper Dih.  Improper Dih.
>>   LJ-14
>>    1.20006e+04    1.92297e+03    5.62600e+03    1.47801e+01
>>   3.67746e+03
>>     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum
>>  En.
>>    2.41174e+04    1.46421e+05   -5.06609e+05   -7.56156e+04
>>  -4.00402e+06
>>      Potential Pressure (bar)
>>   -4.39246e+06   -2.10739e+04
>> 
>>           Step           Time         Lambda
>>              2        2.0        0.0
>> 
>>   Energies (kJ/mol)
>>           Bond          Angle    Proper Dih.  Improper Dih.
>>   LJ-14
>>    1.17961e+04    1.92126e+03    5.62633e+03    1.46477e+01
>>   3.67461e+03
>>     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum
>>  En.
>>    2.41145e+04    1.45528e+05   -5.06679e+05   -7.56315e+04
>>  -4.18671e+06
>>      Potential Pressure (bar)
>>   -4.57635e+06   -2.10854e+04
>> 
>>           Step           Time         Lambda
>>              3        3.0        0.0
>> 
>>           Step           Time         Lambda
>>              4        4.0        0.0
>> 
>>   Energies (kJ/mol)
>>           Bond          Angle    Proper Dih.  Improper Dih.
>>   LJ-14
>>    1.16705e+04    1.92041e+03    5.62652e+03    1.45728e+01
>>   3.67282e+03
>>     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum
>>  En.
>>    2.41128e+04    1.45113e+05   -5.06721e+05   -7.56410e+04
>>  -4.24486e+06
>>      Potential Pressure (bar)
>>   -4.63509e+06   -2.10913e+04
>> 
>>           Step           Time         Lambda
>>              5        5.0        0.0
>> 
>>           Step           Time         Lambda
>>

[gmx-users] Re: g_lie question

2011-11-18 Thread EGY

I see from the file that the units are in KJ/mol, which means my calculations 
are really off. But regardless, I still don't understand what the value in 
parentheses means, like (nan).
If anyone can decipher, please respond. Thank you for your time.
2egy


On Nov 18, 2011, at 11:43 AM, EGY wrote:

> I am trying to figure out how to use the g_lie tool in gromacs. I have the 
> dGbind value for the ligand-solvent interactions and for the protein-ligand 
> complex.
> However, I cannot find in the manual what units these values are. I get the 
> following:
> DGbind = 1953867.080 (0.664)
> and 
> DGbind = 185147.449 (nan)
> 
> What does the parentheses mean and what is (nan)? And, what units are these 
> in?
> 
> Any input would be greatly appreciated.
> Thanks!
> 2egy

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[gmx-users] How DispCorr influsnces pressure

2011-11-18 Thread Dr. Vitaly V. Chaban

Dear all:

Could anybody comment about why "DispCorr=EnerPres" influences
pressure so drastically? For certain system of liquid/vapor interface,
we get P_zz (perpendicular to the interface) = -7 (with correction)
and +4 without correction. The statistics is a few nanoseconds, so
this cannot be just a result of large fluctuations.

Thanks in advance.

-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] How DispCorr influsnces pressure

2011-11-18 Thread David van der Spoel


On 2011-11-18 19:52, Dr. Vitaly V. Chaban wrote:

Dear all:

Could anybody comment about why "DispCorr=EnerPres" influences
pressure so drastically? For certain system of liquid/vapor interface,
we get P_zz (perpendicular to the interface) = -7 (with correction)
and +4 without correction. The statistics is a few nanoseconds, so
this cannot be just a result of large fluctuations.

Thanks in advance.

Dispcorr is only for homogeneous liquids. It should not be used for 
membranes.


--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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[gmx-users] .ppa file

Hello Justin,

I am doing project on afm simulation of protein complex.I have used em.mdp
file for minimization.

Now i am wondering where to use .ppa file for afm parameters.

Can you guide me with files related to afm simulation.


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Re: [gmx-users] How DispCorr influsnces pressure

2011-11-18 Thread Michael Shirts

> Dispcorr is only for homogeneous liquids. It should not be used for
> membranes.

More precisely -- the dispersion correction is an analytical
correction to both the pressure and energy that is rigorously correct
in the limit of the radial distribution function g(r)=1 outside the
van der Waals cutoff.  For a lipid bilayer, this not a good
approximation, since the system is not isotropic.

Since there is not "right" way to do membrane systems currently, the
best bet is to go with the same cutoff treatment the lipids were
parameterized with.

DispCorr = Ener is probably still a good idea, since g(r)=1 isn't
perfect, but it's better than completely ignoring the long range
energy.  DispCorr = Ener will not change the configurations sampled,
so any phase properties, pressures, etc. will be unaffected, but the
results will be somewhat less cutoff dependent.

See:
http://pubs.acs.org/doi/abs/10.1021/jp0735987
for some additional information.

Members of the Gromacs team are working behind the scenes for various
possible solutions to the problem for nonisotropic systems.  Don't
expect anything until 5.0, though.

Best,
Michael
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Re: [gmx-users] Re: g_lie question




EGY wrote:

I see from the file that the units are in KJ/mol, which means my calculations 
are really off. But regardless, I still don't understand what the value in 
parentheses means, like (nan).
If anyone can decipher, please respond. Thank you for your time.


"nan" mean "not a number," indicating something has gone seriously wrong with 
your calculation.  Without more information, it's impossible to say what exactly 
that problem is.


-Justin


2egy


On Nov 18, 2011, at 11:43 AM, EGY wrote:


I am trying to figure out how to use the g_lie tool in gromacs. I have the 
dGbind value for the ligand-solvent interactions and for the protein-ligand 
complex.
However, I cannot find in the manual what units these values are. I get the 
following:
DGbind = 1953867.080 (0.664)
and 
DGbind = 185147.449 (nan)


What does the parentheses mean and what is (nan)? And, what units are these in?

Any input would be greatly appreciated.
Thanks!
2egy




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] .ppa file




ibi2010...@iiita.ac.in wrote:

Hello Justin,

I am doing project on afm simulation of protein complex.I have used em.mdp
file for minimization.

Now i am wondering where to use .ppa file for afm parameters.

Can you guide me with files related to afm simulation.




The .ppa format has not been used in many years.  Versions in the 3.3.x series 
used them, but now all pull code settings are specified in the .mdp file. 
Please see the pulling/umbrella sampling tutorial on the Gromacs website.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] non-specific protein-protein interactions

2011-11-18 Thread Ben Reynwar

On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham  wrote:
> On 18/11/2011 8:10 AM, Ben Reynwar wrote:
>>
>> Dear gromacs list,
>>
>> Does anyone know how well current force fields capture the energetics
>> of non-specific protein-protein interactions?  I'm simulating a
>> protein with an arm that alternates between (apparently) non-specific
>> adsorption to the main-body of the protein and free movement in the
>> solvent.  Can I place any trust in the results of an MD simulation for
>> something like this?  I haven't seen any comparison of experimental
>> results with simulation results of the energetics of non-specific
>> protein-protein interactions so I'm a little skeptical about it.
>> Currently I'm using generalized born implicit solvent, which is
>> perhaps a mistake when solvation energies could be critical to the
>> results.
>>
>
> I'd be very skeptical unless you can observe many adsorption/desorption
> processes and with explicit solvent (though they're probably mutually
> exclusive).
>
> Mark

I think I asked my question poorly.
In a perfect simulation with explicit solvent and infinite sampling,
roughly what kind of error might one expect for peptide-peptide
interaction energies due to the force field?
Presumably there are papers out there that go into this, but I'm not
finding them.  If anyone knows of any directions to point me in, I'd
really appreciate it.

Cheers,
Ben


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[gmx-users] afm simulation

Hello,

I went through the tutorial umbrella sampling and i found that it is
similar to afm simulation only using harmonic potential.

May be i am wrong.Can you just satisfy my curiosity?

Thanx.


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Re: [gmx-users] afm simulation




ibi2010...@iiita.ac.in wrote:

Hello,

I went through the tutorial umbrella sampling and i found that it is
similar to afm simulation only using harmonic potential.

May be i am wrong.Can you just satisfy my curiosity?



They are functional equivalents.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Hbond occupancy

2011-11-18 Thread Larif Sofiene

Greeting 
Is there a value from it we can be sure about hbond existence  in reality.
For example for a hbond occupancy rate of 10% we can say that this hbond has a 
good chance to exist in reality an effectively participate in the protein 
phenomena (movement,structure...) and for another hbond occupancy with 0.7% we 
can safely ignore it because it will not participate in protein behavior.
Is there such level value?-- 
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[gmx-users] REMD: when it exchange the replica, it will be bombed!!

2011-11-18 Thread 杜波

dear teachear,
i do remd in NPT,
when it exchange the replica, it will be bombed!!

step 400, will finish Wed Nov 23 23:21:34 2011
Warning: 1-4 interaction between 1384 and 1396 at distance 140.157 which is
larger than the 1-4 table size 20.895 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

---
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: nsgrid.c, line: 549

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value 175. It should have been within [ 0 .. 168 ]

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

thanks!!!
regards,
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com


md.mdp
Description: Binary data
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Re: [gmx-users] REMD: when it exchange the replica, it will be bombed!!


On 19/11/2011 1:49 PM, 杜波 wrote:

dear teachear,
i do remd in NPT,
when it exchange the replica, it will be bombed!!

step 400, will finish Wed Nov 23 23:21:34 2011
Warning: 1-4 interaction between 1384 and 1396 at distance 140.157 
which is larger than the 1-4 table size 20.895 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

---
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: nsgrid.c, line: 549

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value 175. It should have been within [ 0 .. 168 ]

For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors



Did you check out the information available for this issue there? Does 
your simulation even run without REMD?


Mark
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Re: [gmx-users] non-specific protein-protein interactions


On 19/11/2011 6:42 AM, Ben Reynwar wrote:

On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham  wrote:

On 18/11/2011 8:10 AM, Ben Reynwar wrote:

Dear gromacs list,

Does anyone know how well current force fields capture the energetics
of non-specific protein-protein interactions?  I'm simulating a
protein with an arm that alternates between (apparently) non-specific
adsorption to the main-body of the protein and free movement in the
solvent.  Can I place any trust in the results of an MD simulation for
something like this?  I haven't seen any comparison of experimental
results with simulation results of the energetics of non-specific
protein-protein interactions so I'm a little skeptical about it.
Currently I'm using generalized born implicit solvent, which is
perhaps a mistake when solvation energies could be critical to the
results.


I'd be very skeptical unless you can observe many adsorption/desorption
processes and with explicit solvent (though they're probably mutually
exclusive).

Mark

I think I asked my question poorly.
In a perfect simulation with explicit solvent and infinite sampling,
roughly what kind of error might one expect for peptide-peptide
interaction energies due to the force field?
Presumably there are papers out there that go into this, but I'm not
finding them.  If anyone knows of any directions to point me in, I'd
really appreciate it.


I don't recall having ever seen an explicit solvation simulation on even 
a small peptide that claimed exhaustive sampling, never mind a system 
that shows such complex behaviour. It's possible someone has used 
slow-growth methods to grow a small peptide ligand onto the side of a 
protein, and that could give a guide to the accuracy of inter-protein 
energetics, but I've never gone looking for such.


Mark
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[gmx-users] simulation of a simple, solvated DPPC membrane

2011-11-18 Thread undergrad j

Hello there!

I am an undergraduate working on my thesis, which involves the simulation
of a DPPC membrane. My college is small and the department does not have
experience with MD simulations, so I am 100% on my own. I have successfully
modeled simple proteins in water- but I want to move onto bilayers.

I am attempting to simulate a simple, homogeneous DPPC bilayer. I have a
.pdb file of the membrane, along with .itp files provided by
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. I am
following this procedure for setting up the membrane:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html

However, I feel like I am missing something? The procedure is telling me to
alter a .top file to accommodate the altered force field .itp's (ffG53a6 to
include Berger lipid parameters-which I have already accomplished)- maybe
the .top in question is the topology of the protein that is being implanted
in the membrane? I do not want a membrane bound protein in this simulation-
so how do I generate a .top for a simple membrane? Is it through pdb2gmx?
Do I have to manually program the system topology?

Maybe someone can point me to a detailed procedure for setting up a simple
membrane system from start to finish...?

I am probably going to be bugging this group a lot in the next few weeks-
thank you for reading this

(Sorry if this question is confusing/sounds silly- again, I'm working on my
own)
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Re: [gmx-users] simulation of a simple, solvated DPPC membrane