I want to perform a protein-DNA-ligand complex simulation by gromacs. but my system contain two ligands named PTR and LIG. but when ever i am going to perform the energy minimization.
This is the content of the topology file:
;
; File 'Protein.top' was generated
; By user: arindam (1000)
; On host: localhost.localdomain
; At date: Mon Dec 24 16:49:35 2018
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.6.2
;
; Command line was:
; ./pdb2gmx -ff amber99sb -f duplex.pdb -o Protein2.pdb -p Protein.top -water tip3p -ignh
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"
#include "PTR.itp"
#include "ligand.itp"
; Include chain topologies
#include "Protein_Protein_chain_A.itp"
#include "Protein_DNA_chain_B.itp"
#include "Protein_DNA_chain_C.itp"
#include "Protein_DNA_chain_D.itp"
; Include water topology
#include "amber99sb.ff/tip3p.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 "amber99sb.ff/ions.itp"
[ system ]
; Name
Grunge ROck MAChoS in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
DNA_chain_B 1
DNA_chain_C 1
DNA_chain_D 1
PTR 1
LIG 1
SOL 46535
can anyone tell me the way out?
Best regards.
regenerate the topology and file names seems missing that's why the machine is unable to identify,
redo, hope it gets resolved !!
Actually the problem is on the the presence of two topology files. when no ligand is there the system is nicely simulated.
When the ligand is shown on the topology by #include , that time problem is coming .
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