VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Aug 31 2017 - 09:57:41 CDT

Dear Amin,

QwikMD uses autopsf to generate psf and pdbs. As you saw and JC mentioned,
replacing the temporary topology file used by autopsf listed on the REMARKS
(*_formatted_autopsf-temp.top) by your local topology files gives psfgen
the information regarding your protein.

One thing that you can do is to copy the contents of top_all36_hybrid.inp
(located in the folder of the readcharmmtop plugin - $env(CHARMMTOPDIR)) to
the top_all36_prot.rtf file. Paste the content after all the topologies
listed in top_all36_prot.rtf file, but before the keyword "END". To make
sure that this hack does not influence other simulations that you may
prepare in the future, save this new topology file using a different name
and save in a local folder. Add this new file to the remarks of the psf
file and in principle the errors will be fixed. Please review your
structure carefully after building the structure and have a critical view
of the results.

The errors regarding the missing residues occur during the building of the
non-protein pdb file, and those residues are protein residues. I would
assume that there is not problem in that regard, but, once again, please
check your structure and see if the terminals of the protein are being
created properly.

I hope this helps

Best

João

On Thu, Aug 31, 2017 at 1:29 AM amin sagar <aamin.sagar_at_gmail.com> wrote:

> Thanks for the suggestion. I added those REMARKS to the psf file and now I
> don't get those "Unknown residue type" errors. However I still get the
> error that the first and last residue don't exist. I have checked that they
> do exist in both PDB and PSF. I have posted the error below.
>
> I made the psf file using QuikMD, is it possible that this file is not
> compatible with Alanine scanning plugin?
>
> I also get the error that Residue V2A is not unknown but that residue is
> present in the hybrid topology file.
>
> I would really be thankful for more suggestions.
>
>
> Structure requires EXTended PSF format
> psfgen) total of 0 cross-terms
> psfgen) no residue 145 of segment AP1
> psfgen) Residue AP1:145 not exsisting, skipping patch CTER.
>
> psfgen) no residue 1 of segment AP1
> psfgen) Residue AP1:1 not exsisting, skipping patch NTER.
>
> psfgen) no residue 145 of segment BP1
> psfgen) Residue BP1:145 not exsisting, skipping patch CTER.
>
> psfgen) no residue 1 of segment BP1
> psfgen) Residue BP1:1 not exsisting, skipping patch NTER.
>
> psfgen) Info: psf file complete.
> psfgen) Info: writing pdb file
> /home/srlab/amin/Simulations/SLT1/FEP-try/SLT1_QwikMD-FEP/4-VAL
> VAL2ALA/mtemp-nprot.pdb
> psfgen) Info: pdb file complete.
> psfgen) clearing structure, preserving topology and aliases
> psfgen) building segment AP1
> psfgen) reading residues from pdb file
> /home/srlab/amin/Simulations/SLT1/FEP-try/SLT1_QwikMD-FEP/4-VAL
> VAL2ALA/mtemp-AP1.pdb
> psfgen) extracted 145 residues from pdb file
> psfgen) setting patch for first residue to NONE
> Alanine scan: Residue VAL 4 of segment AP1 is mutated to V2A
> psfgen) mutating residue 4 from VAL to V2A
> psfgen) unknown residue type V2A
> psfgen) setting patch for last residue to NONE
> psfgen) Info: generating structure...psfgen) unknown residue type V2A
>
> Regards,
> Amin
>
> On Wed, Aug 30, 2017 at 6:10 AM, JC Gumbart <gumbart_at_physics.gatech.edu>
> wrote:
>
>> This plugin reads the top of your PSF to determine other topology files
>> it should load. If your psf wasn’t generated by psfgen it may be missing
>> these lines. So add a line like
>> REMARKS topology
>> /Users/gumbart/Documents/Research/toppar/top_all36_prot.rtf
>> that points to the necessary topology file(s).
>>
>> However, this created a different error that required me modifying the
>> plugin code, but then I got no output. So at this point I gave up.
>> Hopefully someone else can chime in.
>>
>> Best,
>> JC
>>
>
>> > On Aug 29, 2017, at 9:37 AM, amin sagar <aamin.sagar_at_gmail.com> wrote:
>> >
>> > Dear All,
>> > I am trying to setup an Alanine scanning FEP simulation using the
>> Alanine Scanning Plugin. I am getting " psfgen) unknown residue type " for
>> all the residues.
>> >
>> > I loaded the psf, pdb and xsc files from an earlier simulation in which
>> the system has my protein, ligand, water and the ions. Are these the
>> correct kind of files?
>> >
>>
> > I am adding all the par_all36* parameters and selecting the
>> top_all36.... hybrid topology file.
>>
>
>> >
>> > I have pasted the first and the last part of the error message below.
>> >
>> > I would be really thankful for any help.
>> >
>> > Regards.
>> > Amin.
>> >
>> >
>> > psfgen) total of 45211 atoms
>> > psfgen) total of 30094 bonds
>> > psfgen) total of 15107 angles
>> > psfgen) total of 132 dihedrals
>> > psfgen) total of 0 impropers
>> > psfgen) total of 0 explicit exclusions
>> > psfgen) Structure requires EXTended PSF format
>> > psfgen) total of 0 cross-terms
>> > psfgen) no residue 145 of segment AP1
>> > psfgen) Residue AP1:145 not exsisting, skipping patch CTER.
>> >
>> > psfgen) no residue 1 of segment AP1
>> > psfgen) Residue AP1:1 not exsisting, skipping patch NTER.
>> >
>> > psfgen) no residue 145 of segment BP1
>> > psfgen) Residue BP1:145 not exsisting, skipping patch CTER.
>> >
>> > psfgen) no residue 1 of segment BP1
>> > psfgen) Residue BP1:1 not exsisting, skipping patch NTER.
>> >
>> > psfgen) Info: psf file complete.
>> > psfgen) Info: writing pdb file
>> /home/srlab/amin/Simulations/SLT1/FEP-try/SLT1_QwikMD-FEP/2-THR
>> THR2ALA/mtemp-nprot.pdb
>> > psfgen) Info: pdb file complete.
>> > psfgen) clearing structure, preserving topology and aliases
>> > psfgen) building segment AP1
>> > psfgen) reading residues from pdb file
>> /home/srlab/amin/Simulations/SLT1/FEP-try/SLT1_QwikMD-FEP/2-THR
>> THR2ALA/mtemp-AP1.pdb
>> > psfgen) unknown residue type MET
>> > psfgen) unknown residue type THR
>> > psfgen) unknown residue type LEU
>> > psfgen) unknown residue type VAL
>> > psfgen) unknown residue type LYS
>> > psfgen) unknown residue type ILE
>> > ..
>> > ..
>> > psfgen) unknown residue type HSD
>> > psfgen) unknown residue type PRO
>> > psfgen) extracted 145 residues from pdb file
>> > psfgen) setting patch for first residue to NONE
>> > Alanine scan: Residue THR 2 of segment AP1 is mutated to T2A
>> > psfgen) mutating residue 2 from THR to T2A
>> > psfgen) unknown residue type T2A
>> > psfgen) setting patch for last residue to NONE
>> > psfgen) Info: generating structure...psfgen) unknown residue type MET
>> > failed!
>> >
>> >
>>
>> --
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3000380