VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue Mar 02 2021 - 07:56:53 CST

That worked perfectly! Thank you so much!
Best,
Eddie

On Tue, Mar 2, 2021 at 5:53 AM Michael Robinson <
michael.robinson1_at_monash.edu> wrote:

> 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!qmD71Y82l47te9gzHh9vXaavNo7e0rY-kFHrxiCO9aKVDC4YpkX_CEkaGrWLKHL4YQ$
>> <https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!uHxWDHcJipmfiK9-sVlkUJELPJvgVAHSyPmcW9VJujdCf7Lbdo2N8rRvxrHQPPlVTg$>
>> <<<<<<<<<<<<<<
>> psfgen) >>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<<
>> psfgen)
>> psfgen) Created by CHARMM version 32 1
>> psfgen) reading topology file toppar/top_all36_lipid.rtf
>>
>> psfgen) \\\\\\\ CHARMM36 All-Hydrogen Lipid Topology File ///////
>> psfgen) All comments and questions should be submitted to the
>> psfgen) parameter forum at the CHARMM website: https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!qmD71Y82l47te9gzHh9vXaavNo7e0rY-kFHrxiCO9aKVDC4YpkX_CEkaGrWLKHL4YQ$
>> <https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!uHxWDHcJipmfiK9-sVlkUJELPJvgVAHSyPmcW9VJujdCf7Lbdo2N8rRvxrHQPPlVTg$>
>> psfgen)
>> psfgen) Created by CHARMM version 36 1
>> psfgen) reading topology file toppar/top_all36_prot.rtf
>>
>> psfgen) >>>>>>>>CHARMM36 All-Hydrogen Topology File for Proteins <<<<<<
>> psfgen) >>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
>> psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> May 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
>> psfgen) All comments to the CHARMM web site: https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!qmD71Y82l47te9gzHh9vXaavNo7e0rY-kFHrxiCO9aKVDC4YpkX_CEkaGrWLKHL4YQ$
>> <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!qmD71Y82l47te9gzHh9vXaavNo7e0rY-kFHrxiCO9aKVDC4YpkX_CEkaGrUnU8ZNTQ$
>> <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
>>
> 

-- 
_________________________________________________________
Edward Ackad, Ph.D <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!qmD71Y82l47te9gzHh9vXaavNo7e0rY-kFHrxiCO9aKVDC4YpkX_CEkaGrXlsQGt_A$ >
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390