[gmx-users] Atomtype CR1 not found

[rainy908]

Hi,

I get the error "Atomtype CR1 not found" when I execute grompp.  After perusing the gmx archives, I understand this error has to do with the lack of "CR1" being specified in the force field.  However, I did include the appropriate .itp files in my .top file (shown below).  As you can see, obviously CR1 is specified in taxol.itp and gtp.itp.  Therefore, I'm not sure what exactly is the problem here.

Any input on this issue would be greatly appreciated.

1JFF.top
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
;       File '1JFF.top' was generated
;       By user: onbekend (0)
;       On host: onbekend
;       At date: Mon Aug 15 17:22:01 2011
;
;       This is a standalone topology file
;
;       It was generated using program:
;       pdb2gmx - VERSION 4.5.3
;
;       Command line was:
;       /software/gromacs/gromacs-4.5.3-x86_64/bin/pdb2gmx -f 1JFF_new.pdb -o 1JFF.gro -p 1JFF.top
;
;       Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
#include "taxol.itp"
#include "gdp.itp"
#include "gtp.itp"

; Include chain topologies
#include "1JFF_Protein_chain_A.itp"
#include "1JFF_Protein_chain_B.itp"
#include "1JFF_Ion_chain_A2.itp"

; Include water topology
#include "oplsaa.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "oplsaa.ff/ions.itp"

[ system ]
; Name
TUBULIN ALPHA CHAIN; TUBULIN BETA CHAIN in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
Ion_chain_A2        1
Taxol               1
GDP                 1
GTP                 1
SOL             21016
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



taxol.itp
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
;       This file was generated by PRODRG version AA081006.0504
;       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
TA1      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CR1     1  TA1     C05     1   -0.015  12.0110
     2        HC     1  TA1     H05     1    0.015   1.0080
     3       CR1     1  TA1     C06     2   -0.012  12.0110
     4        HC     1  TA1     H06     2    0.019   1.0080
     5       CR1     1  TA1     C07     2   -0.012  12.0110
     6        HC     1  TA1     H07     2    0.019   1.0080
     7       CR1     1  TA1     C08     2   -0.012  12.0110
     8        HC     1  TA1     H08     2    0.019   1.0080
     9       CR1     1  TA1     C09     2   -0.012  12.0110
    10        HC     1  TA1     H09     2    0.019   1.0080
    11         C     1  TA1     C04     2   -0.028  12.0110
    12         C     1  TA1     C03     3    0.357  12.0110
    13         O     1  TA1     O03     3   -0.710  15.9994
    14        OA     1  TA1     O02     3   -0.186  15.9994
    15       CH1     1  TA1     C02     3    0.235  13.0190
    16       CH1     1  TA1     C10     3    0.148  13.0190
    17       CH1     1  TA1     C11     3    0.156  12.0110
    18        OA     1  TA1     O04     4   -0.175  15.9994
    19         C     1  TA1     C12     4    0.378  12.0110
    20         O     1  TA1     O05     4   -0.670  15.9994
...
...
<snip>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



gtp.itp
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ moleculetype ]
; Name nrexcl
GTP      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1         O     1  GTP      O6     1   -0.266  15.9994
     2         C     1  GTP      C6     1    0.216  12.0110
     3        NR     1  GTP      N1     1   -0.008  14.0067
     4         H     1  GTP      H1     1   -0.020   1.0080
     5         C     1  GTP      C2     1    0.322  12.0110
     6        NT     1  GTP      N2     1   -0.001  14.0067
     7         H     1  GTP     H22     1   -0.020   1.0080
     8         H     1  GTP     H21     1   -0.020   1.0080
     9        NR     1  GTP      N3     1   -0.203  14.0067
    10         C     1  GTP      C4     2    0.133  12.0110
    11         C     1  GTP      C5     2    0.048  12.0110
    12        NR     1  GTP      N7     2   -0.321  14.0067
    13       CR1     1  GTP      C8     2   -0.037  12.0110
    14        HC     1  GTP      H8     2   -0.019   1.0080
    15        NR     1  GTP      N9     2    0.112  14.0067
    16       CH1     1  GTP     CAU     2    0.084  13.0190
..
..
<snip>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~