From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Mon Oct 19 2020 - 15:45:28 CDT

Hi Gianfranco,

This is what I ended up doing and have shown the results in two previous
emails.

Best,
Bassam

On Mon, Oct 19, 2020 at 1:43 PM Gianfranco Abrusci <
gianfranco.abrusci_at_unitn.it> wrote:

> Hi Bassam,
> since for parm14 ACE is indeed a residue, you should probably have the ACE
> residue in the PDB, but then you should remove the patch from the psfgen
> script and use `first NONE`.
>
> Regards,
> Gianfranco
>
> Il giorno lun 19 ott 2020 alle ore 22:38 Bassam Haddad <bhaddad_at_pdx.edu>
> ha scritto:
>
>> Hi Gianfranco,
>>
>> I attempted what you have suggested originally and it is what lead to my
>> problem initially.
>>
>> Best,
>> Bassam
>>
>>
>>
>>
>>
>> On Mon, Oct 19, 2020 at 1:37 PM Gianfranco Abrusci <
>> gianfranco.abrusci_at_unitn.it> wrote:
>>
>>> Hi Bassam,
>>> I might be wrong, but to my knowledge ACE is not a residue but a patch.
>>> What I would do is to start from a PDB file with 1st residue GLY2, and
>>> then apply the patch to the N-terminus.
>>> I see that the system is a bit more complicated than this single
>>> protein, but you can try only for this small part and see if it works.
>>>
>>> Regards,
>>> Gianfranco
>>>
>>> Il giorno lun 19 ott 2020 alle ore 21:31 Bassam Haddad <bhaddad_at_pdx.edu>
>>> ha scritto:
>>>
>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>
>>> --
>>> Gianfranco Abrusci
>>>
>>
>
> --
> Gianfranco Abrusci
>