Respected Sir, Though im finshed upto production step of protein metal complexes, topology file couldnt be created and there is no information about any atoms in my pdb file. the created topology file are shown below
; ; File 'ebolaag.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Wed Oct 7 16:06:22 2015 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx_d - VERSION 4.5 ; ; Command line was: ; ./pdb2gmx_d -f ebolaag.pdb -o ebolaag.gro -p ebolaag.top -ignh ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" ; Include chain topologies #include "ebolaag_Protein_chain_A.itp" #include "ebolaag_Ion_chain_A2.itp" ; Include water topology #include "oplsaa.ff/tip4p.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 "oplsaa.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_chain_A 1 Ion_chain_A2 1 SOL 4673 I can't understand what is the problem, so pls tell me what could be the reason for this. Sincierly, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.