From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Wed Oct 14 2020 - 19:58:08 CDT

Hi Bassam,

Are there errors earlier? Some of the stream files aren't parsed
properly by psfgen, as they use syntax that is specific to CHARMM (the
program). I'm betting that there is syntax in there that prevents the
ACE patch from being read.

-Josh

On 10/14/20 5:15 PM, Bassam Haddad wrote:
> 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