From: Ramin Ekhteiari (ramin_ekh_at_yahoo.com)
Date: Tue Jul 24 2012 - 06:57:42 CDT

hi
I have problems building the PSF for chain A of  1jNO.pdb.
I got these errors :

*****psfgen) unknown residue type FVA
psfgen) unknown residue type ETA
psfgen) extracted 16 residues from pdb file
psfgen) Info: generating structure...psfgen) unknown residue type FVA
failed!******

my pgn script is  :

# Script to build the protein structure of GA
# Run with "psfgen < <this script> > <logfile>
# Use the specified CHARMM27 topology file.
topology top_all27_prot_lipid.inp
# D-Leucine and D-Valine have the same topology as the
# usual L-Leu and L-Val residues, they're just mirror
# images. Hence we can use the existing topology file.
# We also alias an atom in the ethanolamide residue so
# that psfgen doesn't have to guess the position of the atom.
pdbalias residue DLE LEU
pdbalias residue DVA VAL
pdbalias atom ETA O OG
# Build two segments, one for each chain.
segment GA1 {
first NONE
last NONE
pdb chainA.pdb
}
segment GA2 {
first NONE
last NONE
pdb chainB.pdb
}
# Load the coordinates for each segment.
coordpdb chainA.pdb GA1
coordpdb chainB.pdb GA2
# Write out the psf file
writepsf protein.psf
# Guess the positions of missing atoms. As long as all the heavy
# atoms are present, psfgen usually does a very good job of this.
guesscoord
writepdb protein.pdb

cheers,
  ramin