Dear all gromacs users,
While running the grompp commond after
addition of counter ions i am getting the following error.
Fatal error:
number of coordinates
in coordinate file (3ASW_ion.gro, 178301)
does not
match topology (3ASW.top, 178293)
Here i am sending my .top file,kindly tell me how to overcome this error.
;
; File '3ASW.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Sat Jun 9 10:36:25 2012
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.5
;
; Command line was:
; pdb2gmx -f 3ASW.pdb -o 3ASW.gro -p 3ASW.top -missing
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "gromos43a1.ff/forcefield.itp"
; Include chain topologies
#include "3ASW_Protein_chain_A.itp"
#include "3ASW_Protein_chain_B.itp"
; Include water topology
#include "gromos43a1.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 "gromos43a1.ff/ions.itp"
;#include "ions.itp"
[ system ]
; Name
CLUMPING FACTOR B; TAIL REGION DERIVED PEPTIDE in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
SOL 129
SOL 5
SOL 58209
NA ions 8
/Add NA ions
Suryanarayana Seera,
JRF,
India.
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