[gmx-users] Regarding error

Dallas Warren Dallas.Warren at monash.edu
Fri Jun 8 07:39:32 CEST 2012

Have you incorrectly changed the numbers in the topology, the difference in the number is 8, so it appears your coordinate file contains 8 more atoms than the topology.  You will have to work out how that is.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Seera Suryanarayana
Sent: Friday, 8 June 2012 3:32 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Regarding error

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"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include topology for ions
#include "gromos43a1.ff/ions.itp"
;#include "ions.itp"
[ system ]
; Name

[ 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,
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