Dear all gromacs users,<br><br> While running the grompp commond after addition of counter ions i am getting the following error.<br><br> Fatal error:<br>
number of coordinates in coordinate file (3ASW_ion.gro, 178301)<br> does not match topology (3ASW.top, 178293)<br>
<br>Here i am sending my .top file,kindly tell me how to overcome this error.<br><br><br><br><br><br>;<br>; File '3ASW.top' was generated<br>; By user: onbekend (0)<br>; On host: onbekend<br>; At date: Sat Jun 9 10:36:25 2012<br>
;<br>; This is a standalone topology file<br>;<br>; It was generated using program:<br>; pdb2gmx - VERSION 4.5.5<br>;<br>; Command line was:<br>; pdb2gmx -f 3ASW.pdb -o 3ASW.gro -p 3ASW.top -missing<br>
;<br>; Force field was read from the standard Gromacs share directory.<br>;<br><br>; Include forcefield parameters<br>#include "gromos43a1.ff/forcefield.itp"<br><br>; Include chain topologies<br>#include "3ASW_Protein_chain_A.itp"<br>
#include "3ASW_Protein_chain_B.itp"<br><br>; Include water topology<br>#include "gromos43a1.ff/spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>
; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br><br>; Include topology for ions<br>#include "gromos43a1.ff/ions.itp"<br>;#include "ions.itp"<br>[ system ]<br>
; Name<br>CLUMPING FACTOR B; TAIL REGION DERIVED PEPTIDE in water<br><br>[ molecules ]<br>; Compound #mols<br>Protein_chain_A 1<br>Protein_chain_B 1<br>SOL 129<br>SOL 5<br>SOL 58209<br>
NA ions 8<br>/Add NA ions<br><br><br>Suryanarayana Seera,<br>JRF,<br>India.<br>