On 8/9/19 11:09 AM, afsaneh maleki wrote:
Dear All
I generated topology.top file for Gold surface with g_pdb2gmx -
VERSION 4.5.5 using oplsaa force field as the following:
; Command line was:
; g_pdb2gmx -f Au110.gro -p 1 -o 1
; Force field was read from the standard Gromacs share directory.
; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Ion 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 AU rtp AU q +1.0
1 opls_966 1 AU Au 1 1 196.998 ;
qtot 1
; residue 2 AU rtp AU q +1.0
2 opls_966 2 AU Au 2 1 196.998 ;
qtot 2
.
.
; residue 2400 AU rtp AU q +1.0
2400 opls_966 2400 AU Au 2400 1 196.998 ;
qtot 2400
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
[ system ]
; Name
gold surface (2400 residue)
[ molecules ]
; Compound #mols
Ion 1
After that, I modified topology file hardly:
# mols 1 to #mols 2400 since I had defined 2400 residues.
I don’t know why g_pdb2gmx write one residue in part of [molecules]*?*
You should not do this if there are 2400 particles. pdb2gmx has written
a single [moleculetype] for all of them. Your topology now specifies
2400*2400 particles. The concept of a "molecule" in GROMACS has nothing
to do with chemical features, only what you specify in an input file.
When I try to run g_grompp, it failed with massage:
*Fatal error:*
*Invalid particle type 0.0 on line opls_966 Au 79 196.9940
0.0 3.20000e-01 6.50000e-01*
I moved [atomtype] partition from ffnonbonded.itp to topology file before [
moleculetype ], I again obtained this error.
You need to specify a particle type, e.g. A for atom. See existing lines
for the correct syntax.
-Justin
Any relevant idea is appreciated.
Afsaneh
--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
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