From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Mar 02 2018 - 13:55:19 CST

Hi Peter,

Yes. It is a bit unclear from the manual, but you need to give psfgen some starting coordinates. For proteins with crystal structures, typically this happens with a coordpdb command. So try:

package require psfgen
topology top_all36_prot.rtf

segment P1 {

residue 0 ASP

pdb peptide_noh.pdb

}
coordpdb peptide_noh.pdb P1
guesscoord
writepdb peptide_modified.pdb

-Josh

On 03/02/2018 03:56 AM, Peter Mawanga wrote:
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:

////////////////////////////

package require psfgen
topology top_all36_prot.rtf

segment P1 {

residue 0 ASP

pdb peptide_noh.pdb

}

guesscoord
writepdb peptide_modified.pdb

////////////////////////////

The log:

////////////////////////////

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<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.charmm.org&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C7debeb924194405659a608d5802c3117%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636555849652517271&sdata=BIOlrs42AXxlOon8HtVlbtn9z8Yc%2BnnC9leyvfKWY2k%3D&reserved=0>
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

////////////////////////////

--
Cheers
Peter