From: JC Gumbart (
Date: Tue Aug 29 2017 - 19:40:47 CDT

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.


> On Aug 29, 2017, at 9:37 AM, amin sagar <> 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!