[gmx-users] Regarding error

[Seera Suryanarayana]

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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