From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Mon Oct 19 2020 - 12:38:16 CDT

I have been working through this, and found a potential fix. Amber reads an
Acetylation as a residue, while charmm sees it as a patch. So I have added
the ACE residue to my chains using psfgen, and according to the pdb files
the Acetylation is added. However, I cannot see the acetylation in VMD, and
receive the error message:

Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 1 (none) and 2 (protein)

Where residue 1 is ACE. Below are the sections of my .pdb/.psf to show that
the ACE is indeed in the file, but I cannot see why VMD is having trouble
reading it.

*PDB*
ATOM ***** HY1 ACE A 1 -7.701 3.607 -33.683 1.00 0.00 A1
ATOM ***** CAY ACE A 1 -8.616 3.252 -33.874 1.00 0.00 A1
ATOM ***** HY2 ACE A 1 -9.065 2.990 -33.020 1.00 0.00 A1
ATOM ***** HY3 ACE A 1 -9.159 3.947 -34.345 1.00 0.00 A1
ATOM ***** C ACE A 1 -8.537 2.447 -34.461 1.00 0.00 A1
ATOM ***** O ACE A 1 -8.616 1.531 -34.067 1.00 0.00 A1
ATOM ***** N GLY A 2 -8.323 2.595 -35.783 1.00 0.00 A1
  N
ATOM ***** HN GLY A 2 -7.405 2.545 -36.173 1.00 0.00 A1
ATOM ***** CA GLY A 2 -9.394 2.836 -36.730 1.00 0.00 A1
  C
ATOM ***** HA1 GLY A 2 -9.857 3.773 -36.453 1.00 0.00 A1
ATOM ***** HA2 GLY A 2 -10.024 2.103 -36.699 1.00 0.00 A1
  H
ATOM ***** C GLY A 2 -8.890 2.965 -38.150 1.00 0.00 A1
  C
ATOM ***** O GLY A 2 -8.154 3.897 -38.465 1.00 0.00 A1
  O

*PSF*
  117135 A1 1 ACE HY1 HC 0.112300 1.0080 0
  117136 A1 1 ACE CAY CT -0.366200 12.0100 0
  117137 A1 1 ACE HY2 HC 0.112300 1.0080 0
  117138 A1 1 ACE HY3 HC 0.112300 1.0080 0
  117139 A1 1 ACE C C 0.597200 12.0100 0
  117140 A1 1 ACE O O -0.567900 16.0000 0
  117141 A1 2 GLY N N -0.415700 14.0100 0
  117142 A1 2 GLY HN H 0.271900 1.0080 0
  117143 A1 2 GLY CA CX -0.025200 12.0100 0
  117144 A1 2 GLY HA1 H1 0.069800 1.0080 0
  117145 A1 2 GLY HA2 H1 0.069800 1.0080 0
  117146 A1 2 GLY C C 0.597300 12.0100 0
  117147 A1 2 GLY O O -0.567900 16.0000 0

Is there something obvious I am missing here?

On Wed, Oct 14, 2020 at 6:22 PM Bassam Haddad <bhaddad_at_pdx.edu> wrote:

> 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
>>
>>
>>