Hey all, I'm trying to import energy minimization files into VMD to view and I'm getting some errors. First I note that:
small molecule pdb file shows a total of 48 atoms my new molecule topology (*.itp file, and *.gro file) show 22 atoms, which I thought were non-H atoms My tally of non-H atoms show 21 non-H atoms (16 C's, 4 O's, and 1 N)-What's going on here? My *.ndx file shows 22 atoms I ran grompp and make_ndx using the small molecule gro and itp files generated by PRODRG. Obviously I lost H's when processing the original pdb file in PRODRG (RTM). When reviewing PRODRG website I saw one can use the ADDhyd [atomname] to the input drawing file, but seeing as HETATM already designates the hydrogen this doesn't make sense. In any case, how do I add more than one H to an atom (e.g. methyl group CH2, CH3)? Where do I place these statements in the file? Last, if the input file to PRODRG is fixed, will this allow VMD to run? Any specific examples or guidance on how to protonate atoms in .pdb files would be greatly appreciated. Regards, Marc _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php