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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Seera Suryanarayana Sent: Friday, 8 June 2012 3:32 PM To: gmx-users@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" #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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