Dear all gromacs users,<br><br> After added the counter ions to the top file and further i used 'grompp' commond,i got the following error.<br><br> Fatal error:<br>
moleculetype CU1 is redefined.<br><br> This error occurs due the duplication of CU1 in .top file. But i cannot find that error in my .top file.Here i am sending my .top file. Kindly tell me how to overcome this error.<br>
<br><br><br><br>;<br>; File '1UZ9.top' was generated<br>; By user: onbekend (0)<br>; On host: onbekend<br>; At date: Thu Jun 7 13:55:15 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 1UZ9.pdb -o 1UZ9.gro -p 1UZ9.top<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 "1UZ9_Protein_chain_A.itp"<br>#include "1UZ9_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>Protein in water<br><br>[ molecules ]<br>
; Compound #mols<br>Protein_chain_A 1<br>Protein_chain_B 1<br>SOL 13532<br>NA charge 3<br>/Add NA ions<br><br>Thanks and regards<br><br>Suryanarayana Seera,<br>JRF,<br>India. <br>