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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