From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Wed Oct 14 2020 - 20:22:12 CDT

Hi Josh,

This is the entire output:

vmd > source ../BuildSys_Amber.tcl
To run this program type: run <protein-prefix> <membrane-prefix> <outname>
<isoform(26/46/50)>
vmd > run Cx46 POPC TEST 46
Info) Using plugin pdb for structure file Cx46.pdb
Info) Using plugin pdb for coordinates from file Cx46.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 38628
Info) Bonds: 39204
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 2352
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 24 Protein: 24 Nucleic: 0
psfgen) clearing structure, preserving topology and aliases
Info) Opened coordinate file chain-A1.pdb for writing.
Info) Finished with coordinate file chain-A1.pdb.
Info) Opened coordinate file chain-A2.pdb for writing.
Info) Finished with coordinate file chain-A2.pdb.
Info) Opened coordinate file chain-B1.pdb for writing.
Info) Finished with coordinate file chain-B1.pdb.
Info) Opened coordinate file chain-B2.pdb for writing.
Info) Finished with coordinate file chain-B2.pdb.
Info) Opened coordinate file chain-C1.pdb for writing.
Info) Finished with coordinate file chain-C1.pdb.
Info) Opened coordinate file chain-C2.pdb for writing.
Info) Finished with coordinate file chain-C2.pdb.
Info) Opened coordinate file chain-D1.pdb for writing.
Info) Finished with coordinate file chain-D1.pdb.
Info) Opened coordinate file chain-D2.pdb for writing.
Info) Finished with coordinate file chain-D2.pdb.
Info) Opened coordinate file chain-E1.pdb for writing.
Info) Finished with coordinate file chain-E1.pdb.
Info) Opened coordinate file chain-E2.pdb for writing.
Info) Finished with coordinate file chain-E2.pdb.
Info) Opened coordinate file chain-F1.pdb for writing.
Info) Finished with coordinate file chain-F1.pdb.
Info) Opened coordinate file chain-F2.pdb for writing.
Info) Finished with coordinate file chain-F2.pdb.
Info) Opened coordinate file chain-G1.pdb for writing.
Info) Finished with coordinate file chain-G1.pdb.
Info) Opened coordinate file chain-G2.pdb for writing.
Info) Finished with coordinate file chain-G2.pdb.
Info) Opened coordinate file chain-H1.pdb for writing.
Info) Finished with coordinate file chain-H1.pdb.
Info) Opened coordinate file chain-H2.pdb for writing.
Info) Finished with coordinate file chain-H2.pdb.
Info) Opened coordinate file chain-I1.pdb for writing.
Info) Finished with coordinate file chain-I1.pdb.
Info) Opened coordinate file chain-I2.pdb for writing.
Info) Finished with coordinate file chain-I2.pdb.
Info) Opened coordinate file chain-J1.pdb for writing.
Info) Finished with coordinate file chain-J1.pdb.
Info) Opened coordinate file chain-J2.pdb for writing.
Info) Finished with coordinate file chain-J2.pdb.
Info) Opened coordinate file chain-K1.pdb for writing.
Info) Finished with coordinate file chain-K1.pdb.
Info) Opened coordinate file chain-K2.pdb for writing.
Info) Finished with coordinate file chain-K2.pdb.
Info) Opened coordinate file chain-L1.pdb for writing.
Info) Finished with coordinate file chain-L1.pdb.
Info) Opened coordinate file chain-L2.pdb for writing.
Info) Finished with coordinate file chain-L2.pdb.
psfgen) reading topology file
/home/bassam/toppar_c36_jul20/non_charmm/parm14sb_all.rtf

psfgen) AMBER 2014SB force-field conversion
psfgen) See: http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00255
psfgen) J. Chem. Theory Comput., DOI: 10.1021/acs.jctc.5b00255
psfgen)
psfgen) Created by CHARMM version 23 1
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.
Info) Finished with coordinate file Cx46.pdb.
vmd >

On Wed, Oct 14, 2020 at 5:58 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> 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
>
>
>