[gmx-users] Drug-Enzyme Tutorial

[SWAPNA]

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.