VMD-L Mailing List

From: Gianfranco Abrusci (gianfranco.abrusci_at_unitn.it)
Date: Mon Oct 19 2020 - 15:36:50 CDT

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