[gmx-users] Choosing more PMF-windows

[Shay Teaching]

Dear GROMACS users,

I have recently completed running several PMF-windows.
After viewing the histrogram file it seems that I need better sampling at
some positions, but the histogram file starts at z=0.
Is there any way to prevent g_wham from starting at 0, and instead show the
real Z-coordinates of the selected-group?

Regards,
-Shay
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[gmx-users] Re: Choosing more PMF-windows

[Shay Teaching]

P.S.
Using gromacs 4.0.7

On Sun, Jul 31, 2011 at 5:36 AM, Shay Teaching wrote:

> Dear GROMACS users,
>
> I have recently completed running several PMF-windows.
> After viewing the histrogram file it seems that I need better sampling at
> some positions, but the histogram file starts at z=0.
> Is there any way to prevent g_wham from starting at 0, and instead show the
> real Z-coordinates of the selected-group?
>
> Regards,
> -Shay
>
>
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Re: [gmx-users] Choosing more PMF-windows

[Justin A. Lemkul]

Shay Teaching wrote:

Dear GROMACS users,

I have recently completed running several PMF-windows.
After viewing the histrogram file it seems that I need better sampling 
at some positions, but the histogram file starts at z=0.
Is there any way to prevent g_wham from starting at 0, and instead show 
the real Z-coordinates of the selected-group?




If it starts at zero, then it means your sampling starts at a distance of zero 
along the reaction coordinate.  If this is not what you intended, check your 
input files.


-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] Choosing more PMF-windows

[Shay Teaching]

Distance of zero between COM of pull_group0 and pull_group1?

On Sun, Jul 31, 2011 at 5:46 AM, Justin A. Lemkul  wrote:

>
>
> Shay Teaching wrote:
>
>> Dear GROMACS users,
>>
>> I have recently completed running several PMF-windows.
>> After viewing the histrogram file it seems that I need better sampling at
>> some positions, but the histogram file starts at z=0.
>> Is there any way to prevent g_wham from starting at 0, and instead show
>> the real Z-coordinates of the selected-group?
>>
>>
> If it starts at zero, then it means your sampling starts at a distance of
> zero along the reaction coordinate.  If this is not what you intended, check
> your input files.
>
> -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] Choosing more PMF-windows

[Justin A. Lemkul]

Shay Teaching wrote:

Distance of zero between COM of pull_group0 and pull_group1?



Yes.  The x-axis of the histogram plot indicates the distance along the reaction 
coordinate.


-Justin

On Sun, Jul 31, 2011 at 5:46 AM, Justin A. Lemkul > wrote:




Shay Teaching wrote:

Dear GROMACS users,

I have recently completed running several PMF-windows.
After viewing the histrogram file it seems that I need better
sampling at some positions, but the histogram file starts at z=0.
Is there any way to prevent g_wham from starting at 0, and
instead show the real Z-coordinates of the selected-group?


If it starts at zero, then it means your sampling starts at a
distance of zero along the reaction coordinate.  If this is not what
you intended, check your input files.

-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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--


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] Choosing more PMF-windows

[Shay Teaching]

Ok thanks!

On Sun, Jul 31, 2011 at 5:54 AM, Justin A. Lemkul  wrote:

>
>
> Shay Teaching wrote:
>
>> Distance of zero between COM of pull_group0 and pull_group1?
>>
>>
> Yes.  The x-axis of the histogram plot indicates the distance along the
> reaction coordinate.
>
> -Justin
>
>  On Sun, Jul 31, 2011 at 5:46 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Shay Teaching wrote:
>>
>>Dear GROMACS users,
>>
>>I have recently completed running several PMF-windows.
>>After viewing the histrogram file it seems that I need better
>>sampling at some positions, but the histogram file starts at z=0.
>>Is there any way to prevent g_wham from starting at 0, and
>>instead show the real Z-coordinates of the selected-group?
>>
>>
>>If it starts at zero, then it means your sampling starts at a
>>distance of zero along the reaction coordinate.  If this is not what
>>you intended, check your input files.
>>
>>-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
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>> 
>> >
>>Please search the archive at
>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search
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>> >
>> before posting!
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>>> >.
>>
>>Can't post? Read 
>> http://www.gromacs.org/__**Support/Mailing_Lists
>>
>> 
>> >
>>
>>
>>
> --
> ==**==
>
> 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] umbrella sampling

[chris . neale]

I've never actually reweighted with F-values. These are the values by  
which the component PMFs are shifted during WHAM after debiasing the  
umbrella potentials.


Look at equations 6 and 7 in "The multicanonical weighted histogram  
analysis method for the free-energy landscape along structural  
transition paths" Satoshi Ono, Nobuyuki Nakajima, Junichi Higo and  
Haruki Nakamura


My best guess is that you do it like this:

1. Run 1-D wham and obtain the F-values.

2. create an empty 3D histogram structure for z, rgyrA, and rgyrB.

3. Go through the data from each window and add a value to the  
appropriate location for [z,rgyrA,rgyrB]. This value is not the  
integer count 1. This value that you add to each histogram bin is a  
real number:


  1 * exp(-(1/RT)*-F) * exp(-(1/RT)*0.5K*(z-z0)^2

4. Now convert your histogram of probabilities to free energies dG=-RTln(P)

** To test this, project your 3-D free energy profile onto each  
dimension successively and compare it to (z) the profile from 1-D  
wham, and (rgyrA or rgyrB) the profile from 2-D wham with zero force  
constants as I outlined in my previous post.


PLEASE NOTE: this email outlines an *idea* of how to accomplish what  
you want. You must check the match for yourself.


Chris.

Qian Wang qwang at mail.uh.edu
Sat Jul 30 18:05:33 CEST 2011

* Previous message: [gmx-users] umbrella sampling
* Next message: [gmx-users] OPLSAA parameters
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Thanks very much.
I am sorry I did not describe my question very clear. In my system, I  
am going to obtain three things. (1) the free energy versus distance,  
which I can obtain from g_wham. (2) the free energy versus, eg, the  
radius of gyration of the object A. (3) the 2-D free energy as a  
function of the radius of gyration of A and the radius of gyration of  
B. I do not know how to get (2) and (3).
Your first method can help me obtain (2), but I can not obtain (3)  
because then it needs a 3-D WHAM code, am I correct? For your second  
method, I do not quite understand how to re-weighting using the  
F-values from 1D-WHAM. Could you please explain it? Thanks.


Sincerely,
Qian

- Original Message -
From: chris.neale at utoronto.ca
Date: Friday, July 29, 2011 11:00 pm
Subject: [gmx-users] umbrella sampling
To: gmx-users at gromacs.org

format your data for 2D-WHAM with 1D being the distance and the  
2nd-D being your other coordinate of interest. Specify a value of  
zero for the force constants for your 2nd-D. Run 2D-WHAM. Boltzmann  
project the 2D PMF onto your 2nd-D.


I think you can also do essentially the same thing by re-
weighting using the F-values from 1D-WHAM, but I find the above  
method to be the simplest. It also provides you with a 2D free  
energy profile, which can be informative both biologically and to  
indicate on sampling problems.


Note that you're very likely going to run into convergence problems  
since your 2nd-D will rely on brute-force to converge, and worse:  
the umbrellas in 1D can force the sampling in the 2nd-
D to surmount energy barriers that might be circumvented in  
unrestrained sampling.


Chris.

-- original message --

Qian Wang wrote:



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[gmx-users] Re: PRODRG tools

[Andrej Frolov]

Hello,

There are several ways to get the topology + force field for an 
arbitrary molecule:


1. "Maestro + Desmond" programs of the Schrodinger software pack can 
assign OPLS-AA force filed. The parameters are stored in the *.cms file.
2. "FFLD_SERVER" of the Schrodinger software: 
$SCHRODINGER/utilities/ffld_server. Also OPLS-AA force filed.
You will need to write a script which converts the output to 
Gromacs format.
3. "antechamber" + "tleap" of the AmberTools utilities. It can assign 
any kind of Amber force field, like General Amber Force Field.

See an example:http://compchemmpi.wikispaces.com/Scripts#GenAmberTop
 You could use the "amb2gmx" script to convert the generated Amber 
topology to Gromacs format:

http://ffamber.cnsm.csulb.edu/ffamber-tools.html
4. ''PRODRG server'' for the united atom GMX force fields.
5. ''Vega ZZ'' and "Vega" can assign OPLS-AA force field, but not all 
atom types, bonds etc. are supported.
6.  "MCCCS Towhee'' monte carlo code can assign very many force fields, 
but, first, one has to create the so-called basic connectivity map 
(which atom is covalently bound to which).

http://towhee.sourceforge.net/

Kind regards,
Andrey
--
Andrey Frolov
PhD student
Max Planck Institute for Mathematics in the Sciences
(MPI f. Mathematik in den Naturwissenschaften)
Inselstr. 22-26, 04103 Leipzig, Germany
e-mail: fro...@mis.mpg.de
web: http://www.mis.mpg.de/scicomp/CompPhysChem/GroupMain.html



Dear all,

Is there any other free tool  like PRODRG ?  PRODRG server couldn't read
PDB file from user any more. It 's not easy to get a free version asap.

   Best

   Shiyong



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Re: [gmx-users] umbrella sampling

[Qian Wang]

thanks very much. I will test it. 
 
Sincerely,
Qian

- Original Message -
From: chris.ne...@utoronto.ca
Date: Sunday, July 31, 2011 8:58 am
Subject: [gmx-users] umbrella sampling
To: gmx-users@gromacs.org

> I've never actually reweighted with F-values. These are the 
> values by which the component PMFs are shifted during WHAM after 
> debiasing the umbrella potentials.
> 
> Look at equations 6 and 7 in "The multicanonical weighted 
> histogram analysis method for the free-energy landscape along 
> structural transition paths" Satoshi Ono, Nobuyuki Nakajima, 
> Junichi Higo and Haruki Nakamura
> 
> My best guess is that you do it like this:
> 
> 1. Run 1-D wham and obtain the F-values.
> 
> 2. create an empty 3D histogram structure for z, rgyrA, and rgyrB.
> 
> 3. Go through the data from each window and add a value to the 
> appropriate location for [z,rgyrA,rgyrB]. This value is not the 
> integer count 1. This value that you add to each histogram bin 
> is a real number:
> 
>   1 * exp(-(1/RT)*-F) * exp(-(1/RT)*0.5K*(z-z0)^2
> 
> 4. Now convert your histogram of probabilities to free energies 
> dG=-RTln(P)
> 
> ** To test this, project your 3-D free energy profile onto each 
> dimension successively and compare it to (z) the profile from 1-
> D wham, and (rgyrA or rgyrB) the profile from 2-D wham with zero 
> force constants as I outlined in my previous post.
> 
> PLEASE NOTE: this email outlines an *idea* of how to accomplish 
> what you want. You must check the match for yourself.
> 
> Chris.
> 
> Qian Wang qwang at mail.uh.edu
> Sat Jul 30 18:05:33 CEST 2011
> 
> * Previous message: [gmx-users] umbrella sampling
> * Next message: [gmx-users] OPLSAA parameters
> * Messages sorted by: [ date ] [ thread ] [ 
> subject ] [ author ]
> 
> Thanks very much.
> I am sorry I did not describe my question very clear. In my 
> system, I am going to obtain three things. (1) the free energy 
> versus distance, which I can obtain from g_wham. (2) the free 
> energy versus, eg, the radius of gyration of the object A. (3) 
> the 2-D free energy as a function of the radius of gyration of A 
> and the radius of gyration of B. I do not know how to get (2) 
> and (3).
> Your first method can help me obtain (2), but I can not obtain 
> (3) because then it needs a 3-D WHAM code, am I correct? For 
> your second method, I do not quite understand how to re-
> weighting using the F-values from 1D-WHAM. Could you please 
> explain it? Thanks.
> 
> Sincerely,
> Qian
> 
> - Original Message -
> From: chris.neale at utoronto.ca
> Date: Friday, July 29, 2011 11:00 pm
> Subject: [gmx-users] umbrella sampling
> To: gmx-users at gromacs.org
> 
> >format your data for 2D-WHAM with 1D being the distance and the 
> 2nd-D being your other coordinate of interest. Specify a value 
> of zero for the force constants for your 2nd-D. Run 2D-WHAM. 
> Boltzmann project the 2D PMF onto your 2nd-D.
> >
> >I think you can also do essentially the same thing by re-
> >weighting using the F-values from 1D-WHAM, but I find the above 
> method to be the simplest. It also provides you with a 2D free 
> energy profile, which can be informative both biologically and 
> to indicate on sampling problems.
> >
> >Note that you're very likely going to run into convergence 
> problems since your 2nd-D will rely on brute-force to converge, 
> and worse: the umbrellas in 1D can force the sampling in the 2nd-
> >D to surmount energy barriers that might be circumvented in 
> unrestrained sampling.
> >
> >Chris.
> >
> >-- original message --
> >
> >Qian Wang wrote:
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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Re: [gmx-users] OPLSAA parameters

[Elisabeth]

Thanks Justin for your guidance. By following your tips, I have now all the
parameters I need... Please let me know if I am missing any [ angletypes ]
or [ dihedraltypes ] for a hydrocarbon molecule.

Best,

[ bondtypes ]
;  i j func b0   kb
  CTCT  10.15290   224262.4   ; CHARMM 22 parameter file
  CTHC  10.10900   284512.0   ; CHARMM 22 parameter file

[ angletypes ]
;i  j k  func   th0   cth
CT CT CT  1   112.700488.273   ; CHARMM 22 parameter file
CT CT HC  1   110.700313.800   ; CHARMM 22 parameter file
HC CT HC  1   107.800276.144   ; CHARMM 22 parameter file

[ dihedraltypes ]
  CT CT CT CT  3  2.92880  -1.46440   0.20920
-1.67360   0.0   0.0 ; hydrocarbon all-atom
  CT CT CT HC  3  0.62760   1.88280   0.0
-2.51040   0.0   0.0 ; hydrocarbon all-atom
  HC CT CT HC  3  0.62760   1.88280   0.0
-2.51040   0.0   0.0 ; hydrocarbon *new* 11/99





On 30 July 2011 07:40, Justin A. Lemkul  wrote:

>
>
> Elisabeth wrote:
>
>> Hello to all,
>>
>> I am looking for bonded and nonbonded parameters for C H atoms in
>> saturated hydrocarbons.
>>
>> atom types are:
>> Carbon atoms opls_135  opls_136 H  opls_140
>>  opls_135   12.01100  ; alkane CH3
>>  opls_136   12.01100  ; alkane CH2
>>  opls_1401.00800  ; alkane H.
>>
>> Please help me out with the following:
>>
>> - I am wondering if I am selecting the correct values, for C-C and C-H
>> bonds from ffoplsaabon.itp.
>>
>>
> The C-C bond is not correct for alkanes.  It is for the C-C bond of oxalic
> acid, as the comment indicates.  In ffnonbonded.itp, you can see how opls_*
> types are mapped to different bonded atom types (for instance, opls_135/136
> are CT).  Note that in the topology, you do not have to explicitly define
> values when using OPLS-AA; any bond between two defined bonded atom types
> will be automatically detected and used.
>
>
>  C C   10.15100   292880.0   ; wlj oxalic acid, etc.
>> HCC   10.10900   284512.0   ; wlj 7/96
>>
>> - what does wlj mean?
>>
>>
> Probably someone's initials, which occur frequently to indicate either the
> source of the parameters or the individual that added them.  In this case,
> my guess would be Jorgensen is the referenced individual here.
>
>  - what are the units?
>>
>>
> This is in the manual.
>
>
>
>> Angle
>>
>>  CA CA CZ  1   120.000585.760   ; wlj
>>  CA CA CR  1   120.000527.184   ;
>>  CA CA CX  1   120.000711.280   ;
>>  C  CT Cl  1   109.800577.392   ; wlj
>>
>> - I can not distinguish CA CZ  What are they referring to?
>>
>>
> See the above tip about converting atom types in ffnonbonded.itp.
>
>
>  [ dihedraltypes ]
>>
>>  C  C  CT HC  3  0.17782   0.53346   0.0  -0.71128
>>   0.0   0.0 ; dicarbonyls BMC 8,1881(2000)
>>
>> - Is this what I need for oplsaa 135 136 140?
>>
>>
> Probably not.  The comment indicates the dihedral is for dicarbonyls.  The
> appropriate dihedral is:
>
>  CT CT CT HC  3  0.62760   1.88280   0.0  -2.51040
> 0.0   0.0 ; hydrocarbon all-atom
>
> Note how the comment indicates it is for use with hydrocarbons.  Again,
> like bonds as described above, you do not need to explicitly list parameters
> in the topology.  They will be inferred from the atom types.
>
>
>  ffoplsaanb.itp.
>>
>>  opls_135   CT6 12.01100-0.180   A3.5e-01
>>  2.76144e-01
>>  opls_136   CT6 12.01100-0.120   A3.5e-01
>>  2.76144e-01
>>
>>  opls_140   HC1  1.00800 0.060   A2.5e-01
>>  1.25520e-01
>>
>> - are these parameters for
>>
>>  opls_135   12.01100  ; alkane CH3
>>  opls_136   12.01100  ; alkane CH2
>>  opls_1401.00800  ; alkane H.
>>
>> ?
>>
>>
> Yes.
>
>
>  Also in usr/local/gromacs/share/**gromacs/top/ directory  I can not find
>> ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in previous versions
>> these files were accessible. I am using itp files from version 4.0.7 and
>> wanted to make sure the above parameters for oplsa_135 oplsa_136 and
>> oplsa_140 have been remained unchanged in 4.5.4. Where can I find these
>> files?
>>
>>
> The force field organization has changed, but the content of the force
> fields has not.  This is described in the manual.  All the equivalent files
> are now in the oplsaa.ff subdirectory.  For backwards compatibility, the
> statement #include "ffoplsaa.itp" will indeed call the force field, because
> you will note that ffoplsaa.itp now simply calls the correct force field
> with #include "oplsaa.ff/forcefield.itp."
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[

Re: Re: [gmx-users] OPLSAA parameters

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Re: [gmx-users] OPLSAA parameters

[Justin A. Lemkul]

Elisabeth wrote:
Thanks Justin for your guidance. By following your tips, I have now all 
the parameters I need... Please let me know if I am missing any [ 
angletypes ] or [ dihedraltypes ] for a hydrocarbon molecule.




Seems fine to me; grompp will complain if something is missing.  Is there a 
reason that you're trying to parse out certain parameters?  It'd be far easier 
to just #include "oplsaa.ff/forcefield.itp" in your topology and have the entire 
OPLS-AA force field available to you, rather than reinventing the wheel.


-Justin


Best,

[ bondtypes ]
;  i j func b0   kb
  CTCT  10.15290   224262.4   ; CHARMM 22 parameter file
  CTHC  10.10900   284512.0   ; CHARMM 22 parameter file

[ angletypes ]
;i  j k  func   th0   cth
CT CT CT  1   112.700488.273   ; CHARMM 22 parameter file
CT CT HC  1   110.700313.800   ; CHARMM 22 parameter file
HC CT HC  1   107.800276.144   ; CHARMM 22 parameter file

[ dihedraltypes ]
  CT CT CT CT  3  2.92880  -1.46440   0.20920  
-1.67360   0.0   0.0 ; hydrocarbon all-atom
  CT CT CT HC  3  0.62760   1.88280   0.0  
-2.51040   0.0   0.0 ; hydrocarbon all-atom
  HC CT CT HC  3  0.62760   1.88280   0.0  
-2.51040   0.0   0.0 ; hydrocarbon *new* 11/99






On 30 July 2011 07:40, Justin A. Lemkul > wrote:




Elisabeth wrote:

Hello to all,

I am looking for bonded and nonbonded parameters for C H atoms
in saturated hydrocarbons.

atom types are:
Carbon atoms opls_135  opls_136 H  opls_140
 opls_135   12.01100  ; alkane CH3

 opls_136   12.01100  ; alkane CH2
 opls_1401.00800  ; alkane H.

Please help me out with the following:

- I am wondering if I am selecting the correct values, for C-C
and C-H bonds from ffoplsaabon.itp.


The C-C bond is not correct for alkanes.  It is for the C-C bond of
oxalic acid, as the comment indicates.  In ffnonbonded.itp, you can
see how opls_* types are mapped to different bonded atom types (for
instance, opls_135/136 are CT).  Note that in the topology, you do
not have to explicitly define values when using OPLS-AA; any bond
between two defined bonded atom types will be automatically detected
and used.


C C   10.15100   292880.0   ; wlj oxalic acid, etc.
HCC   10.10900   284512.0   ; wlj 7/96

- what does wlj mean?


Probably someone's initials, which occur frequently to indicate
either the source of the parameters or the individual that added
them.  In this case, my guess would be Jorgensen is the referenced
individual here.

- what are the units?


This is in the manual.



Angle

 CA CA CZ  1   120.000585.760   ; wlj
 CA CA CR  1   120.000527.184   ;
 CA CA CX  1   120.000711.280   ;
 C  CT Cl  1   109.800577.392   ; wlj

- I can not distinguish CA CZ  What are they referring to?


See the above tip about converting atom types in ffnonbonded.itp.


[ dihedraltypes ]

 C  C  CT HC  3  0.17782   0.53346   0.0
 -0.71128   0.0   0.0 ; dicarbonyls BMC 8,1881(2000)

- Is this what I need for oplsaa 135 136 140?


Probably not.  The comment indicates the dihedral is for
dicarbonyls.  The appropriate dihedral is:

 CT CT CT HC  3  0.62760   1.88280   0.0
 -2.51040 0.0   0.0 ; hydrocarbon all-atom

Note how the comment indicates it is for use with hydrocarbons.
 Again, like bonds as described above, you do not need to explicitly
list parameters in the topology.  They will be inferred from the
atom types.


ffoplsaanb.itp.

 opls_135   CT6 12.01100-0.180   A  
 3.5e-01  2.76144e-01
 opls_136   CT6 12.01100-0.120   A  
 3.5e-01  2.76144e-01


 opls_140   HC1  1.00800 0.060   A  
 2.5e-01  1.25520e-01


- are these parameters for

 opls_135   12.01100  ; alkane CH3
 opls_136   12.01100  ; alkane CH2
 opls_1401.00800  ; alkane H.

?


Yes.


Also in usr/local/gromacs/share/__gromacs/top/ directory  I can
not find ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in
previous versions these files were accessible. I am using itp
files from version 4.0.7 and wanted to make sure the above
parameters for oplsa_135 oplsa_136 and oplsa_140 have been
remained unchanged in 4.5.4. Where can I find these files?


The force field organization has changed, but the content o

[gmx-users] protein ligand

[Ragothaman Yennamalli]

Hi,

I know this is off topic. Can someone please suggest independent scoring
functions that can calculate binding energies between protein and ligand?

Thanks and Regards,
Ragothaman
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Re: [gmx-users] OPLSAA parameters

[Elisabeth]

Hi Justin,

So far I have been #including ffoplsaa.itp and running simulations. The
reason I was after parameters is just to have a better indea on the FF
parameters rather than just using them blindly, that's it :)

Thank you,

On 31 July 2011 20:03, Justin A. Lemkul  wrote:

>
>
> Elisabeth wrote:
>
>> Thanks Justin for your guidance. By following your tips, I have now all
>> the parameters I need... Please let me know if I am missing any [ angletypes
>> ] or [ dihedraltypes ] for a hydrocarbon molecule.
>>
>>
> Seems fine to me; grompp will complain if something is missing.  Is there a
> reason that you're trying to parse out certain parameters?  It'd be far
> easier to just #include "oplsaa.ff/forcefield.itp" in your topology and have
> the entire OPLS-AA force field available to you, rather than reinventing the
> wheel.
>
> -Justin
>
>  Best,
>>
>> [ bondtypes ]
>> ;  i j func b0   kb
>>  CTCT  10.15290   224262.4   ; CHARMM 22 parameter file
>>  CTHC  10.10900   284512.0   ; CHARMM 22 parameter file
>>
>> [ angletypes ]
>> ;i  j k  func   th0   cth
>> CT CT CT  1   112.700488.273   ; CHARMM 22 parameter file
>> CT CT HC  1   110.700313.800   ; CHARMM 22 parameter file
>> HC CT HC  1   107.800276.144   ; CHARMM 22 parameter file
>>
>> [ dihedraltypes ]
>>  CT CT CT CT  3  2.92880  -1.46440   0.20920  -1.67360
>>   0.0   0.0 ; hydrocarbon all-atom
>>  CT CT CT HC  3  0.62760   1.88280   0.0  -2.51040
>>   0.0   0.0 ; hydrocarbon all-atom
>>  HC CT CT HC  3  0.62760   1.88280   0.0  -2.51040
>>   0.0   0.0 ; hydrocarbon *new* 11/99
>>
>>
>>
>>
>>
>> On 30 July 2011 07:40, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Elisabeth wrote:
>>
>>Hello to all,
>>
>>I am looking for bonded and nonbonded parameters for C H atoms
>>in saturated hydrocarbons.
>>
>>atom types are:
>>Carbon atoms opls_135  opls_136 H  opls_140
>> opls_135   12.01100  ; alkane CH3
>> opls_136   12.01100  ; alkane CH2
>> opls_1401.00800  ; alkane H.
>>
>>Please help me out with the following:
>>
>>- I am wondering if I am selecting the correct values, for C-C
>>and C-H bonds from ffoplsaabon.itp.
>>
>>
>>The C-C bond is not correct for alkanes.  It is for the C-C bond of
>>oxalic acid, as the comment indicates.  In ffnonbonded.itp, you can
>>see how opls_* types are mapped to different bonded atom types (for
>>instance, opls_135/136 are CT).  Note that in the topology, you do
>>not have to explicitly define values when using OPLS-AA; any bond
>>between two defined bonded atom types will be automatically detected
>>and used.
>>
>>
>>C C   10.15100   292880.0   ; wlj oxalic acid, etc.
>>HCC   10.10900   284512.0   ; wlj 7/96
>>
>>- what does wlj mean?
>>
>>
>>Probably someone's initials, which occur frequently to indicate
>>either the source of the parameters or the individual that added
>>them.  In this case, my guess would be Jorgensen is the referenced
>>individual here.
>>
>>- what are the units?
>>
>>
>>This is in the manual.
>>
>>
>>
>>Angle
>>
>> CA CA CZ  1   120.000585.760   ; wlj
>> CA CA CR  1   120.000527.184   ;
>> CA CA CX  1   120.000711.280   ;
>> C  CT Cl  1   109.800577.392   ; wlj
>>
>>- I can not distinguish CA CZ  What are they referring to?
>>
>>
>>See the above tip about converting atom types in ffnonbonded.itp.
>>
>>
>>[ dihedraltypes ]
>>
>> C  C  CT HC  3  0.17782   0.53346   0.0
>> -0.71128   0.0   0.0 ; dicarbonyls BMC 8,1881(2000)
>>
>>- Is this what I need for oplsaa 135 136 140?
>>
>>
>>Probably not.  The comment indicates the dihedral is for
>>dicarbonyls.  The appropriate dihedral is:
>>
>> CT CT CT HC  3  0.62760   1.88280   0.0
>> -2.51040 0.0   0.0 ; hydrocarbon all-atom
>>
>>Note how the comment indicates it is for use with hydrocarbons.
>> Again, like bonds as described above, you do not need to explicitly
>>list parameters in the topology.  They will be inferred from the
>>atom types.
>>
>>
>>ffoplsaanb.itp.
>>
>> opls_135   CT6 12.01100-0.180   A
>> 3.5e-01  2.76144e-01
>> opls_136   CT6 12.01100-0.120   A
>> 3.5e-01  2.76144e-01
>>
>> opls_140   HC1  1.00800 0.060   A
>> 2.5e-01  1.25520e-01
>>
>>- are these parameters for
>>
>> opls_135   12.01100  ; alkane CH3
>> opls_136   12.01100  ; alkane CH2
>> opls_1401.00800  ; alkane H.
>

Re: [gmx-users] protein ligand

[Mark Abraham]

On 1/08/2011 10:19 AM, Ragothaman Yennamalli wrote:

Hi,

I know this is off topic. Can someone please suggest independent 
scoring functions that can calculate binding energies between protein 
and ligand?


Surely there's a whole literature on this to search for...

Mark
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