VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Mon Jan 13 2020 - 17:20:32 CST

Hello
Several years ago I built a phosphorylated serine residue. After a few years some files disappeared and now I am trying to recreate a psf file from a pdb file that has this altered serine.
My results are interesting when I include the rtf file for the altered residue.

If I keep the default rtf files that are populated in the automatic psf builder and then add SSR_2.rtf and load these files I get three segments. In the past I thought that I just edited the first segment to include all the atoms and deleted the extra two segments. Today this generates a pdb file that is missing the altered residue.
If I included all segments and remove the NTER and CTER patches for the two protein segments i get a pdb file that is missing the bonds to the altered residue and the CTER and NTER patches are still present.

I am using 1.9.3 as installed on our institutional linux clusters.

Is there a step that I am forgetting?
brian