From: amin sagar (aamin.sagar_at_gmail.com)
Date: Tue Aug 29 2017 - 08:37:47 CDT

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!