VMD-L Mailing List

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Wed Oct 14 2020 - 18:15:45 CDT

Hello VMDers,

I would like to test a few different forcefields (parm14sb, opls, charmm)
on my electric field simulations, but am running into errors in building
the simulation input files (PSF). I have chosen to use the charmm-formated
force-fields in the 'non_charmm' folder of the charmm36-jul2020 folder. My
protein requires an n-terminal acetylation, and despite ACE being defined
in parm14sb_all.rtf I am getting errors when trying to construct the .psf.

*Here is a section of my script that I believe is causing the issue:*

  topology /home/bassam/toppar_c36_jul20/non_charmm/parm14sb_all.rtf
  foreach segn $segN {
    resetpsf
    pdbalias residue HIS HID
    segment $segn {
      first ACE
      last NONE
      pdb chain-$segn.pdb
    }
    coordpdb chain-$segn.pdb $segn
    guesscoord
    writepdb chain-$segn.pdb
    writepsf chain-$segn.psf
  }

*Here is the Error message:*

psfgen) clearing structure, preserving topology and aliases
psfgen) aliasing residue HIS to HID
psfgen) building segment A1
psfgen) setting patch for first residue to ACE
psfgen) setting patch for last residue to NONE
psfgen) reading residues from pdb file chain-A1.pdb
psfgen) extracted 108 residues from pdb file
psfgen) Info: generating structure...psfgen) Info: skipping improper
C-CA-N-HN 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 CA-N-C-O 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.
psfgen) unknown patch type ACE
failed!
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

For what it is worth, the script I am using works without fail for
*top_all36_prot.rtf.*

Please advise on how to set the system up correctly.

Thank you!
________________________
*Bassam Haddad*
Ruth L. Kirschstein NRSA Fellow
Doctoral Candidate
Portland State University
Portland, OR