[gmx-users] gromos96 forcefield
Thomas Schlesier
schlesi at uni-mainz.de
Tue May 13 19:15:40 CEST 2008
First of all, thanks for the answers.
So, i get my coordinate-file from the prodrg-beta server (with the gromos96 force field; ffG534a1). This file i edited so that it looks like the format of a .g96 file:
TITLE
linker ohne benzol
END
POSITION
1 ZUG CAA 1 4.918583393 6.143541813 4.921333790
2 UNK CAB 2 4.990583420 6.018541813 4.972333431
2 UNK CAC 3 4.918583393 5.893541813 4.921333790
2 UNK CAD 4 4.990583420 5.767541885 4.972333431
2 UNK CAE 5 4.918583393 5.642541885 4.921333790
2 UNK CAF 6 4.990583420 5.517541885 4.972333431
2 UNK CAG 7 4.918583393 5.392541885 4.921333790
3 HSA NAH 8 4.987583160 5.272542000 4.970333576
3 HSA HAP 9 5.011583328 5.264541626 5.067333698
3 HSA CAI 10 5.022583485 5.164541721 4.877333641
3 HSA OAJ 11 4.993583202 5.174541950 4.758333683
3 HSA NAK 12 5.091583252 5.044541836 4.926333427
3 HSA HAR 13 5.115583420 4.970541954 4.862333775
3 HSA HAQ 14 5.115583420 5.036541939 5.023333549
4 REF CAA 15 4.943583488 4.024541855 4.961333752
5 UNL CAB 16 4.965583324 4.149541855 5.012333393
5 UNL CAC 17 4.943583488 4.274541855 4.961333752
6 HSB NAD 18 4.962583542 4.394541740 5.010333538
6 HSB HAH 19 4.986583233 4.468542099 4.946333408
6 HSB CAE 20 4.997583389 4.406541824 5.152333736
6 HSB OAF 21 4.968583584 4.316541672 5.230333328
6 HSB NAG 22 5.066583633 4.526541710 5.201333523
6 HSB HAJ 23 5.090583324 4.534542084 5.298333645
6 HSB HAI 24 5.090583324 4.600542068 5.138333321
END
BOX
10.000000000 10.000000000 10.000000000
END
The coordinate-file had from prodrg only three numbers after the 'point' because the .g96 file has the format 15.9 i added six 0's and then used editconf to change the box.
The .itp file for one molecule looks:
;
;
; This file was generated by PRODRG version AA080107.0543
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; Name nrexcl
UNL 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 UNL CAA 1 0.064 15.0350
2 CH2 1 UNL CAB 1 0.084 14.0270
3 CH2 1 UNL CAC 1 0.084 14.0270
4 N 1 UNL NAD 1 0.120 14.0067
5 H 1 UNL HAH 1 -0.010 1.0080
6 C 1 UNL CAE 1 0.351 12.0110
7 O 1 UNL OAF 1 -0.715 15.9994
8 NT 1 UNL NAG 1 0.044 14.0067
9 H 1 UNL HAJ 1 -0.011 1.0080
10 H 1 UNL HAI 1 -0.011 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAA
2 3 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAC
3 4 2 0.147 8710000.0 0.147 8710000.0 ; CAC NAD
4 5 2 0.100 18700000.0 0.100 18700000.0 ; NAD HAH
6 4 2 0.134 10500000.0 0.134 10500000.0 ; CAE NAD
6 7 2 0.123 16600000.0 0.123 16600000.0 ; CAE OAF
6 8 2 0.133 10600000.0 0.133 10600000.0 ; CAE NAG
8 9 2 0.100 18700000.0 0.100 18700000.0 ; NAG HAJ
8 10 2 0.100 18700000.0 0.100 18700000.0 ; NAG HAI
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; CAA NAD
2 5 1 ; CAB HAH
2 6 1 ; CAB CAE
3 7 1 ; CAC OAF
3 8 1 ; CAC NAG
4 9 1 ; NAD HAJ
4 10 1 ; NAD HAI
5 7 1 ; HAH OAF
5 8 1 ; HAH NAG
7 9 1 ; OAF HAJ
7 10 1 ; OAF HAI
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 109.5 520.0 109.5 520.0 ; CAA CAB CAC
2 3 4 2 109.5 520.0 109.5 520.0 ; CAB CAC NAD
3 4 5 2 115.0 460.0 115.0 460.0 ; CAC NAD HAH
3 4 6 2 122.0 700.0 122.0 700.0 ; CAC NAD CAE
5 4 6 2 123.0 415.0 123.0 415.0 ; HAH NAD CAE
4 6 7 2 124.0 730.0 124.0 730.0 ; NAD CAE OAF
4 6 8 2 120.0 670.0 120.0 670.0 ; NAD CAE NAG
7 6 8 2 124.0 730.0 124.0 730.0 ; OAF CAE NAG
6 8 9 2 120.0 390.0 120.0 390.0 ; CAE NAG HAJ
6 8 10 2 120.0 390.0 120.0 390.0 ; CAE NAG HAI
9 8 10 2 120.0 445.0 120.0 445.0 ; HAJ NAG HAI
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
4 3 5 6 2 0.0 167.4 0.0 167.4 ; imp NAD CAC HAH CAE
6 4 7 8 2 0.0 167.4 0.0 167.4 ; imp CAE NAD OAF NAG
8 6 10 9 2 0.0 167.4 0.0 167.4 ; imp NAG CAE HAI HAJ
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih NAD CAC CAB CAA
2 3 4 6 1 180.0 1.0 6 180.0 1.0 6 ; dih CAB CAC NAD CAE
8 6 4 3 1 180.0 33.5 2 180.0 33.5 2 ; dih NAG CAE NAD CAC
4 6 8 10 1 180.0 33.5 2 180.0 33.5 2 ; dih NAD CAE NAG HAI
The .itp file for the ohter molecule (the alkane chain is 4 atoms longer) looks really the same but the charges are a little bit different.
So, have i done this right, or are there any mistakes (expect for the charge, see below)?
One thing which i find strange are the charge of two atoms (but that this problem can occur was mentioned)
4 N 1 UNL NAD 1 0.120 14.0067
5 H 1 UNL HAH 1 -0.010 1.0080
The N has an positive charge and the H which is bonded to the N has an negative charge, i expected the different. So i think i must refine the charges, but how?
Look in the paper of the force field and search there how the things were parameteriziesd?
The other question that i have is, what is the difference between the .gro and the .g96 file?
I thought .gro is for the gromos87 force field and .g96 is for all the gromos96 force fields.
But prodrg gives me for both force field an coordinate file which looks from the format like a .gro file.
And on the internet i found an tutorial (http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.html) in which pdb2gmx was used for an gromos96 force field but the
coordinate file was in the end a .gro file
-> so i am some what confused
Thomas
> Message: 1
> Date: Fri, 9 May 2008 14:43:04 +0200
> From: Thomas Schlesier <schlesi at uni-mainz.de>
> Subject: [gmx-users] gromos96 forcefield
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID: <482446D8.3070102 at uni-mainz.de>
> Content-Type: text/plain; charset="ISO-8859-15"
>
> dear all,
> till now i simulated with the gromos87 forcefield, but now i want to
> change it.
> i have two small molecules which consist of a short alkane chain and
> then an urea-group.
>
> i built my molecules with spartan and saved them as .pdb then i tried
> pdb2gmx, but this failed:
> Fatal error:
> Residue 'UNK' not found in residue topology database
> but i have no idea how i should name the residues so that they are found
> in the database.
> then i tried pdb2gmx with my .gro file (which i get from prodrg with the
> .pdb file), but here the same problem occured.
>
> the other thing that i tried was to make the files with the beta version
> of prodrg. i get the .gro/.g96 and .itp files but they look the same
> like the files for the gromos87 forcefield (different values but the
> same format).
> i used editconf on the .g96 file but it doesn't really work, the new
> .g96 file looks like:
>
> TITLE
>
> END
> POSITION
> END
> BOX
> 10.000000000 10.000000000 10.000000000
> END
>
> from that and the gromacs-user manual i get the idea that .gro and .96
> files use different formats, but i don't really know how the format for
> .g96 looks like (i looked for a user manual for gromos96, but didn't
> found one for free).
>
> so the question is:
> 1) is there a way to translate the gromos87 files to gromos96?
> or
> 2) what should i do with the files form prodrg beta that they work?
>
> thanks for an answer
> thomas
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 9 May 2008 08:54:55 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] gromos96 forcefield
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1210337695.4824499f76762 at webmail.vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Quoting Thomas Schlesier <schlesi at uni-mainz.de>:
>
>
>> dear all,
>> till now i simulated with the gromos87 forcefield, but now i want to
>> change it.
>> i have two small molecules which consist of a short alkane chain and
>> then an urea-group.
>>
>> i built my molecules with spartan and saved them as .pdb then i tried
>> pdb2gmx, but this failed:
>> Fatal error:
>> Residue 'UNK' not found in residue topology database
>> but i have no idea how i should name the residues so that they are found
>> in the database.
>> then i tried pdb2gmx with my .gro file (which i get from prodrg with the
>> .pdb file), but here the same problem occured.
>>
>
> Right, because pdb2gmx does not magically produce parameters for any molecule
> you'd like. Check the .rtp file for the force field you're interested in; it
> will show you the residues/molecules for which parameters exist.
>
>
>> the other thing that i tried was to make the files with the beta version
>> of prodrg. i get the .gro/.g96 and .itp files but they look the same
>> like the files for the gromos87 forcefield (different values but the
>> same format).
>>
>
> They should look the same; the different parameters are what you're after. Be
> aware that PRODRG produces charges/charge groups that are often unsatisfactory
> and need refining.
>
>
>> i used editconf on the .g96 file but it doesn't really work, the new
>> .g96 file looks like:
>>
>> TITLE
>>
>> END
>> POSITION
>> END
>> BOX
>> 10.000000000 10.000000000 10.000000000
>> END
>>
>> from that and the gromacs-user manual i get the idea that .gro and .96
>> files use different formats, but i don't really know how the format for
>> .g96 looks like (i looked for a user manual for gromos96, but didn't
>> found one for free).
>>
>> so the question is:
>> 1) is there a way to translate the gromos87 files to gromos96?
>> or
>> 2) what should i do with the files form prodrg beta that they work?
>>
>
> I'm not quite sure what you're after in these, but I can tell you the following:
>
> 1. You don't translate one force field to another, in terms of some simple
> conversion. You derive new parameters, or use parameters from a
> well-documented, trusted source. In terms of .g96 --> .gro conversion,
> editconf should have done the trick. What was the command you tried, and was
> the .g96 file properly formatted?
>
> 2. You use the .itp file you get from PRODRG, verify the validity of the
> parameters, and proceed.
>
> -Justin
>
>
>> thanks for an answer
>> thomas
>> _______________________________________________
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>>
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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