[gmx-users] Drug-Enzyme Tutorial

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jan 8 13:09:34 CET 2008 

Hi Swapna,

The PRODRG server generates topologies for the gmx force field (ffgmx;
deprecated!). You most likely want to have a topology compliant with the
Gromos96 force fields (e.g. ffG43a2). For this you need to use the beta
version of the PRODRG server.

Mind you that force field parameterization is a field of its own and not for
the faint of heart. PRODRG may be good for for some things, but I wouldn't
blindly go with the results obtained. Check
http://wiki.gromacs.org/index.php/Parameterization

Cheers,

Tsjerk

On Jan 8, 2008 12:43 PM, SWAPNA <swapna.lekkala at gmail.com> wrote:

> Hi,
> I am doing the Kerrigan Drug-enzyme tutorial.
> I could generate the drg.itp, drg.gro files using PRODRG server.
> When I use the grompp step before the energy minimization I encounter a
> problem
> --------------------------------
> A fatal error was shown: atom types CB, CR61 and OS were not found.
>
> -------------------------------
> These atom types CB, CR61 and OS are present in the drg.itp file. I
> included the drg.itp file to the trp.top file before submission for
> preprocesing using grompp.
>
> I have checked with atom types present in the forcefield files of my
> gromacs version and found that these are not present in my force field
> files.
>
> What should I do to eliminate the error?
>
> Can you please give me the other corresponding atom types that may be
> used for these unrecognised atom types?
>
>
>
> the drg.itp file that I used with the atom types CB, CR61 and OS
> --------------------------------------------------------------------------
> ;
> ;
> ;       This file was generated by PRODRG version 061128.0522
> ;       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
> IN4      3
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>     1        NT     1  IN4      N3     1    0.144  14.0067
>     2         H     1  IN4     HAA     1    0.072   1.0080
>     3         H     1  IN4     HAB     1    0.072   1.0080
>     4        CB     1  IN4     C20     1    0.423  12.0110
>     5        NT     1  IN4      N4     1    0.145  14.0067
>     6         H     1  IN4     HAF     1    0.072   1.0080
>     7         H     1  IN4     HAE     1    0.072   1.0080
>     8        CB     1  IN4      C6     2    0.000  12.0110
>     9      CR61     1  IN4      C5     2    0.000  13.0190
>    10      CR61     1  IN4      C1     3    0.000  13.0190
>    11      CR61     1  IN4      C2     3    0.000  13.0190
>    12      CR61     1  IN4      C3     3    0.000  13.0190
>    13        CB     1  IN4      C4     3    0.000  12.0110
>    14       CH1     1  IN4     C10     3    0.000  13.0190
>    15       CH2     1  IN4     C14     4    0.131  14.0270
>    16         C     1  IN4     C22     4    0.469  12.0110
>    17         O     1  IN4      O3     4   -0.576  15.9994
>    18        OS     1  IN4      O4     4   -0.113  15.9994
>    19       CH3     1  IN4      C8     4    0.089  15.0350
>    20       CH2     1  IN4      C9     5    0.000  14.0270
>    21       CH2     1  IN4     C11     5    0.000  14.0270
>    22        CB     1  IN4     C12     5    0.000  12.0110
>    23      CR61     1  IN4     C19     5    0.000  13.0190
>    24      CR61     1  IN4     C17     5    0.000  13.0190
>    25      CR61     1  IN4      C7     6    0.000  13.0190
>    26      CR61     1  IN4     C13     6    0.000  13.0190
>    27        CB     1  IN4     C15     6    0.000  12.0110
>    28        CB     1  IN4     C16     7    0.423  12.0110
>    29        NT     1  IN4      N1     7    0.144  14.0067
>    30         H     1  IN4     HAH     7    0.072   1.0080
>    31         H     1  IN4     HAG     7    0.072   1.0080
>    32        NT     1  IN4      N2     7    0.145  14.0067
>    33         H     1  IN4     HAD     7    0.072   1.0080
>    34         H     1  IN4     HAC     7    0.072   1.0080
>
>
> Thanks!!
>
> Swapna
> --
> The logic of life lies exclusively neither in the most incredible
> detail, nor in the most sweeping synopsis.
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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