VMD-L Mailing List

From: amin sagar (aamin.sagar_at_gmail.com)
Date: Thu Aug 31 2017 - 01:28:35 CDT

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!
> >
> >
>
>