Dear all gromacs users, After added the counter ions to the top file and further i used 'grompp' commond,i got the following error.
Fatal error: moleculetype CU1 is redefined. 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. ; ; File '1UZ9.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Jun 7 13:55:15 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f 1UZ9.pdb -o 1UZ9.gro -p 1UZ9.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "gromos43a1.ff/forcefield.itp" ; Include chain topologies #include "1UZ9_Protein_chain_A.itp" #include "1UZ9_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 Protein in water [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 SOL 13532 NA charge 3 /Add NA ions Thanks and regards Suryanarayana Seera, JRF, India.
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