VMD-L Mailing List
From: Gianfranco Abrusci (gianfranco.abrusci_at_unitn.it)
Date: Mon Oct 19 2020 - 15:43:46 CDT
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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
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