Dear all, i m doing mmpbsa calculation using GMXPBSA tool ,for protein ligand complex during the steps i invoked the command pdb2gmx -f _comp0.pdb -p topol_comp.top -i posre_comp.itp -o _comp0.gro -ignh -water tip3p
i have generated the ligand topology such as *.itp and *.prm file ,but it looks like i cant insert those in topology as doing usually ,in order to edit topology database,can anyone give me the details of *.hdb file example VAL 5 1 1 HN N -C CA 1 5 HA CA N C CB 1 5 HB CB CA CG1 CG2 3 4 HG1 CG1 CB CA 3 4 HG2 CG2 CB CA what is HN N -C CA? is there any automatic tool for this available? forcefield charmm36 -- Ragards, Nikhil Maroli -- 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.
