VMD-L Mailing List

From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Tue Mar 02 2021 - 05:53:35 CST

Professor Ackad,

I think the issue is likely to be in the topology file - to bond to the
next residue needs to be explicitly included. In the section detailing your
bonds, you'll need to include that bond - you can look in the existing
CHARMM topology files for examples, but the addition of the following line
in your bond section should be sufficient (provided you're using the
standard backbone atom names):

BOND C +N

Hopefully that's helpful,
Regards,
Michael Robinson

On Tue, 2 Mar 2021 at 07:46, Prof. Eddie <eackad_at_siue.edu> wrote:

> 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!rkVbOi5QkuEjD0lOLTgg236sFPWr1cb9fXmmj8IfFQTbs7Sn6i3ZwUYo5uUsK9Brvw$
> <https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!uHxWDHcJipmfiK9-sVlkUJELPJvgVAHSyPmcW9VJujdCf7Lbdo2N8rRvxrHQPPlVTg$>
> <<<<<<<<<<<<<<
> psfgen) >>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<<
> psfgen)
> psfgen) Created by CHARMM version 32 1
> psfgen) reading topology file toppar/top_all36_lipid.rtf
>
> psfgen) \\\\\\\ CHARMM36 All-Hydrogen Lipid Topology File ///////
> psfgen) All comments and questions should be submitted to the
> psfgen) parameter forum at the CHARMM website: https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!rkVbOi5QkuEjD0lOLTgg236sFPWr1cb9fXmmj8IfFQTbs7Sn6i3ZwUYo5uUsK9Brvw$
> <https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!uHxWDHcJipmfiK9-sVlkUJELPJvgVAHSyPmcW9VJujdCf7Lbdo2N8rRvxrHQPPlVTg$>
> psfgen)
> psfgen) Created by CHARMM version 36 1
> psfgen) reading topology file toppar/top_all36_prot.rtf
>
> psfgen) >>>>>>>>CHARMM36 All-Hydrogen Topology File for Proteins <<<<<<
> psfgen) >>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
> psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> May 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
> psfgen) All comments to the CHARMM web site: https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!rkVbOi5QkuEjD0lOLTgg236sFPWr1cb9fXmmj8IfFQTbs7Sn6i3ZwUYo5uUsK9Brvw$
> <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!rkVbOi5QkuEjD0lOLTgg236sFPWr1cb9fXmmj8IfFQTbs7Sn6i3ZwUYo5uWuk1N1mw$
> <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
>