[gmx-users] chloroform - oplsaa
Chris Neale
chris.neale at utoronto.ca
Tue Jan 29 21:11:25 CET 2008
The error message already tells you what is going wrong:
Invalid order for directive atomtypes, file ""/usr/local/gromacs/share/gromacs/top/chcl3.itp"", line 1
so what is the first line from /usr/local/gromacs/share/gromacs/top/chcl3.itp ?
It's [ atomtypes ]
This is a parameter definition and should come before topology definition.
Therefore move this section to come right after you include ffoplsaa.itp
###############################
; Include water topology
#include "chcl3.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
###############################
I further note that you have not included any CCl3 molecules in your topology, you should do this:
[ molecules ]
; Compound #mols
Protein 1
CCl3 512 ;; or whatever your number is
##############################
Obviously I have not touched on residue 'FEN', a nonstandard oplsaa residue that I know nothing about.
Why did pdb2gmx not generate a topology that was error-free? Because it (and other tools such as genbox, genion)
are designed for proteins in water with ions. Anything non-standard is going to require an enhanced understanding of
input files and I therefore suggest that you read the topology section of the manual much more closely before proceeding.
You would have found your answer on pg 98 and 109 of the gromacs-3.3 manual.
Chris.
---original message---
Hi all,
I'm trying to run a simulation of a phenol in chloroform with the oplsaa forcefield.
I've downloaded the chloroform box from gromacs and added the files to the top folder.
Everything is fine till I run grompp which says:
Fatal error:
Invalid order for directive atomtypes, file ""/usr/local/gromacs/share/gromacs/top/chcl3.itp"", line 1
After downloading the chcl3 box should i have to modify something else?
I've checked in the manual but I'm not able to understand what i'm doing wrong.
This is the top file of my phenol I get after running pdb2gmx:
;
; File 'fenolo.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Fri Jan 25 15:47:30 2008
;
; This is your topology file
; "Ramones For Ever" (P.J. Van Maaren)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 opls_145 1 FEN CG 1 -0.193 12.011 ; qtot -0.193
2 opls_145 1 FEN CD2 2 -0.1642 12.011 ; qtot -0.3572
3 opls_145 1 FEN CE2 3 -0.3176 12.011 ; qtot -0.6748
4 opls_166 1 FEN CZ 4 0.5484 12.011 ; qtot -0.1264
5 opls_145 1 FEN CE1 5 -0.3953 12.011 ; qtot -0.5217
6 opls_145 1 FEN CD1 6 -0.0852 12.011 ; qtot -0.6069
7 opls_146 1 FEN HD2 7 0.171 1.008 ; qtot -0.4359
8 opls_146 1 FEN HE1 8 0.163 1.008 ; qtot -0.2729
9 opls_146 1 FEN HE2 9 0.1907 1.008 ; qtot -0.0822
10 opls_146 1 FEN HD1 10 0.1506 1.008 ; qtot 0.0684
11 opls_146 1 FEN HG 11 0.1496 1.008 ; qtot 0.218
12 opls_167 1 FEN OH 12 -0.6515 15.9994 ; qtot -0.4335
13 opls_168 1 FEN HH 13 0.4334 1.008 ; qtot -0.0001
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 6 1
1 11 1
2 3 1
2 7 1
3 4 1
3 9 1
4 5 1
4 12 1
5 6 1
5 8 1
6 10 1
12 13 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 8 1
1 9 1
2 5 1
2 10 1
2 12 1
3 6 1
3 8 1
3 11 1
3 13 1
4 7 1
4 10 1
5 9 1
5 11 1
5 13 1
6 7 1
6 12 1
7 9 1
7 11 1
8 10 1
8 12 1
9 12 1
10 11 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 6 1
2 1 11 1
6 1 11 1
1 2 3 1
1 2 7 1
3 2 7 1
2 3 4 1
2 3 9 1
4 3 9 1
3 4 5 1
3 4 12 1
5 4 12 1
4 5 6 1
4 5 8 1
6 5 8 1
1 6 5 1
1 6 10 1
5 6 10 1
4 12 13 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
6 1 2 3 3
6 1 2 7 3
11 1 2 3 3
11 1 2 7 3
2 1 6 5 3
2 1 6 10 3
11 1 6 5 3
11 1 6 10 3
1 2 3 4 3
1 2 3 9 3
7 2 3 4 3
7 2 3 9 3
2 3 4 5 3
2 3 4 12 3
9 3 4 5 3
9 3 4 12 3
3 4 5 6 3
3 4 5 8 3
12 4 5 6 3
12 4 5 8 3
3 4 12 13 3
5 4 12 13 3
4 5 6 1 3
4 5 6 10 3
8 5 6 1 3
8 5 6 10 3
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "chcl3.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
fenolo in chcl3
[ molecules ]
; Compound #mols
Protein 1
Thanks in advance
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