Dear gmx users,
I have a problem about the topology output of pdb2gmx. There is a formyl residue as N-terminal in my .pdb file. I know that the pdb file is correct in agreement with RCSB .pdb files. The force field I have to use is gmx ( I need to regenerate some results ), so I defined the formyl residue as a new residue in gmx force field. But when I get the output of pdb2gmx the topology shows that the N atom of the next residue has 3 H atoms ,I think It means that the formyl residue is not connected to the next residue ( here: Valine ). As a result the total charge derived by pdb2gmx is +2e and it is not correct regards to the protein structure. I don't know what is the problem? Is it related to the force field files? Please help me with your suggestions. I would appreciate you. Sincerely, Shima -- 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
