Dear Gromacs Users, I have generated the topology and parameters files for my ligand through swiss param site. Now i am trying to run a simulation of protein ligand complex in POPC bilayer using OPLS force field in Gromacs, but when I am using the grompp command in gromacs for tpr generation I am getting an error as follows:
Atomtype C5A not found Please let me know your suggestions, to correct this error, I have included ligand.itp in the topology file of the protein. Thanks, ram grompp -f mdions.mdp -c combi.gro -p topol.top -o combi.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14# checking input for internal consistency... NOTE 1 [file mdions.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. processing topology... Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaabon.itp Generated 348195 of the 348195 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 348005 of the 348195 1-4 parameter combinations Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/tip3p.itp Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ions.itp ------------------------------------------------------- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 947 Fatal error: Atomtype C5A not found -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
