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 d...@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>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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