VMD-L Mailing List

From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Fri Mar 02 2018 - 04:05:45 CST

Hello VMD users

I am trying to add an ASP residue at the N-terminus of a peptide. Although
the addition is working, but PSFGEN is not able to guess the coordinates of
the new file.

The command:

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package require psfgen
topology top_all36_prot.rtf

segment P1 {

residue 0 ASP

pdb peptide_noh.pdb
}

guesscoord
writepdb peptide_modified.pdb

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The log:

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psfgen) reading topology file top_all36_prot.rtf

psfgen) >>>>>>>>CHARMM36 All-Hydrogen Topology File for Proteins <<<<<<
psfgen) >>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> May 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
psfgen) All comments to the CHARMM web site: www.charmm.org
psfgen) parameter set discussion forum
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) ERROR! Failed to parse autogenerate statement.
psfgen) cross-term entries present in topology definitions

psfgen) building segment P1
psfgen) reading residues from pdb file peptide_noh.pdb
psfgen) extracted 16 residues from pdb file
psfgen) Info: generating structure...psfgen) Info: skipping improper
N-C-CA-HN at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
psfgen) Info: skipping bond C-N at end of segment.
psfgen) Info: skipping improper C-CA-N-O at end of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
psfgen) Info: skipping conformation N-CA-C-O at end of segment.
psfgen) Info: skipping conformation N-CA-C-N at end of segment.
segment complete.
psfgen) Info: guessing coordinates for 277 atoms (129 non-hydrogen)
psfgen) Warning: failed to guess coordinates for 277 atoms

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-- 
Cheers
Peter