From: Prof. Eddie (eackad_at_siue.edu)
Date: Mon Mar 01 2021 - 14:10:15 CST

Hi all,
I was following this
<https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/0432.html>
thread to perform the psfgen on the console so I can insert a mutate
command. In my case I'm using a custom residue and also include the
topology for the residue. It all works fine and doesn't give any errors,
but it will not join my residue (the mutated 215) to the next residue (216)
in the C-N bond. It joins correctly to the previous residue.
Does anyone know how I can fix this, or at least track the error in the
backbone joining down? Barring that, any idea what is the best way to
insert the bond? Manually editing the psf seems to be the only way but then
there are a lot of dihedrals to put in and it means anything similar in the
future will also need a manual process so I'd love to solve it once and for
all.
The output of psfgen is below.
Thanks!
Eddie

psfgen) reading topology file toppar/top_all36_cgenff.rtf

psfgen)
--------------------------------------------------------------------------
 *
psfgen) CGenFF: Topology for the Charmm General Force Field v.
4.4 *
psfgen) for Small Molecule Drug Design
           *
psfgen)
--------------------------------------------------------------------------
 *
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) reading topology file toppar/top_all36_carb.rtf

psfgen) $Id: top_allxx_sugar.inp,v 1.106 2014/08/19 19:07:43 alex Exp $
psfgen) >>>>>>>>>>>> All-hydrogen topologies used in the <<<<<<<<<<<<<<<<
psfgen) >>>>> development of the CHARMM carbohydrate force field<<<<<<<<
psfgen) >>>>>>>>>>>>>>>>>>>>>>>>> June 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
psfgen) >>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<<
psfgen) >>>>>>>>>> via the CHARMM web site: https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!uHxWDHcJipmfiK9-sVlkUJELPJvgVAHSyPmcW9VJujdCf7Lbdo2N8rRvxrHQPPlVTg$ <<<<<<<<<<<<<<
psfgen) >>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<<
psfgen)
psfgen) Created by CHARMM version 32 1
psfgen) reading topology file toppar/top_all36_lipid.rtf

psfgen) \\\\\\\ CHARMM36 All-Hydrogen Lipid Topology File ///////
psfgen) All comments and questions should be submitted to the
psfgen) parameter forum at the CHARMM website: https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!uHxWDHcJipmfiK9-sVlkUJELPJvgVAHSyPmcW9VJujdCf7Lbdo2N8rRvxrHQPPlVTg$
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) reading topology file toppar/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: https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!uHxWDHcJipmfiK9-sVlkUJELPJvgVAHSyPmcW9VJujdCf7Lbdo2N8rRvxrHQPPlVTg$
psfgen) parameter set discussion forum
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) cross-term entries present in topology definitions
psfgen) reading topology file toppar/top_interface.rtf

psfgen) INTERFACE FF
psfgen) topology for nanomaterials
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) reading topology file toppar/pgm_backbone_protein.top

psfgen) Toppar stream file generated by
psfgen) CHARMM General Force Field (CGenFF) program version 2.4.0
psfgen) For use with CGenFF version 4.4
psfgen)
psfgen) reading topology from stream file
psfgen) Topologies generated by
psfgen) CHARMM General Force Field (CGenFF) program version 2.4.0
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) skipping parameters in stream file
psfgen) Parameters generated by analogy by
psfgen) CHARMM General Force Field (CGenFF) program version 2.4.0
psfgen)
psfgen) aliasing residue HIS to HSE
psfgen) aliasing residue ILE atom CD1 to CD
psfgen) building segment P1
psfgen) reading residues from pdb file protein_only.pdb
psfgen) extracted 499 residues from pdb file
psfgen) mutating residue 215 from PHE to PGM
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) reading coordinates from pdb file protein_only.pdb for segment P1
psfgen) Warning: failed to set coordinate for atom CG PHE:215 P1
psfgen) Warning: failed to set coordinate for atom CD1 PHE:215 P1
psfgen) Warning: failed to set coordinate for atom HD1 PHE:215 P1
psfgen) Warning: failed to set coordinate for atom CE1 PHE:215 P1
psfgen) Warning: failed to set coordinate for atom HE1 PHE:215 P1
psfgen) Warning: failed to set coordinate for atom CZ PHE:215 P1
psfgen) Warning: failed to set coordinate for atom HZ PHE:215 P1
psfgen) Warning: failed to set coordinate for atom CD2 PHE:215 P1
psfgen) Warning: failed to set coordinate for atom HD2 PHE:215 P1
psfgen) Warning: failed to set coordinate for atom CE2 PHE:215 P1
psfgen) Warning: failed to set coordinate for atom HE2 PHE:215 P1
psfgen) Info: guessing coordinates for 54 atoms (24 non-hydrogen)
psfgen) Info: writing pdb file p450_prot_apo_pgm215.pdb
psfgen) Info: Atoms with guessed coordinates will have occupancy of 0.0.
psfgen) Info: pdb file complete.
psfgen) Info: writing psf file p450_prot_apo_pgm215.psf
psfgen) total of 8164 atoms
psfgen) total of 8264 bonds
psfgen) total of 15058 angles
psfgen) total of 22138 dihedrals
psfgen) total of 1302 impropers
psfgen) total of 0 explicit exclusions
psfgen) Structure requires EXTended PSF format
psfgen) total of 496 cross-terms
psfgen) Info: psf file complete.
Info) ======================
Info) Please cite TopoTools as:
Info) Axel Kohlmeyer & Josh Vermaas, (2019). TopoTools: Release 1.8
Info) https://urldefense.com/v3/__https://doi.org/10.5281/zenodo.598373__;!!DZ3fjg!uHxWDHcJipmfiK9-sVlkUJELPJvgVAHSyPmcW9VJujdCf7Lbdo2N8rRvxrFOtIGyAQ$
Info) ======================

-- 
_________________________________________________________
Edward Ackad, Ph.D <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!uHxWDHcJipmfiK9-sVlkUJELPJvgVAHSyPmcW9VJujdCf7Lbdo2N8rRvxrFD7XQCUA$ >
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390