hi sorry 4 not doing it before, right now am doing "Solvate the Box" step in molecular modelling am using Gromacs 4.5.5 ver
during the first step i.e "creating the topology file ",i tried to create the topology file by using the command "pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.pdb –p fws.top" for which gromacs showed me an error saying "atomtypeXX not found in the residue type database " i resolved this issue by going through gromacs manual by adding the missing atoms to the dna.rtp file and new atoms to atomtypes.atp file after which it produced the topology file int he next step i setup an box with the command "editconf -bt cubic –f fws.pdb –o fws.pdb -c –d 0.9" in the third step i.e "Solvate the Box" i used the command "genbox –cp fws.pdb –cs spc216.gro –o fws_b4em.pdb –p fws.top" in the fourth step i.e "Setup the energy minimization." i used the command "grompp –f em.mdp –c fws_ion.pdb –p fws.top –o fws_em.tpr" where its givving me an errror which says "Fatal error: Unknown bond_atomtype O2" based on your replies i tried by adding the atom to ffbonded.itp file but it dint work. am attachning my dna.rtp ,atomtypes.atp,ffbonded .itp files please help -ram http://gromacs.5086.n6.nabble.com/file/n4998335/dna.rtp dna.rtp http://gromacs.5086.n6.nabble.com/file/n4998335/ffbonded.itp ffbonded.itp http://gromacs.5086.n6.nabble.com/file/n4998335/atomtypes.atp atomtypes.atp -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998335.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
