psfgen - any version capable of reading extended PSF files?

From: Bjoern Olausson (
Date: Fri Feb 11 2011 - 05:47:05 CST


is there any version of "psfgen" which can read the extended CHARMM PSF file

I converted my PSF files to the standard format, but this resulted in a PSF
files with "duplicates" - too much Atoms *sigh*

I can't use CHARMM to merge the two structures into on because the maximum
bond count is exceeded - I am already using xxlarge version, huge won't
compile :-(

Any workarounds?
My didn't work (Generating an entirely new psf/pdb with psfgen from spitted
PDB files each containing a single segment. But even this works only for the
membrane + protein + some waters. At a certain point it just kills water
because of "duplicate residue key")

I need those merged files for FEP (Just in case anyone is wondering).


This is the psfgen script I tried to merge the files:
topology ../top_all27_prot_lipid.rtf
topology ../toppar_all27_lipid_cholesterol.str

segment PROA {pdb run000_proa.pdb}
segment PROB {pdb run000_prob.pdb}
segment PROC {pdb run000_proc.pdb}
segment PROD {pdb run000_prod.pdb}
segment MEMA {first NONE ; last NONE ; pdb run000_memb.pdb}
segment WATA {first NONE ; last NONE ; pdb run000_tip3.pdb}
segment POTA {first NONE ; last NONE ; pdb run000_pot.pdb}
segment CLAA {first NONE ; last NONE ; pdb run000_cla.pdb}

segment PROE {pdb run270_proa.pdb}
segment PROF {pdb run270_prob.pdb}
segment PROG {pdb run270_proc.pdb}
segment PROH {pdb run270_prod.pdb}
segment MEMB {first NONE ; last NONE ; pdb run270_memb.pdb}
segment WATB {first NONE ; last NONE ; pdb run270_tip3.pdb}
segment POTB {first NONE ; last NONE ; pdb run270_pot.pdb}
segment CLAB {first NONE ; last NONE ; pdb run270_cla.pdb}

coordpdb run000_proa.pdb PROA
coordpdb run000_prob.pdb PROB
coordpdb run000_proc.pdb PROC
coordpdb run000_prod.pdb PROD
coordpdb run000_memb.pdb MEMA
coordpdb run000_tip3.pdb WATA
coordpdb run000_pot.pdb POTA
coordpdb run000_cla.pdb CLAA

coordpdb run000_proa.pdb PROE
coordpdb run000_prob.pdb PROF
coordpdb run000_proc.pdb PROG
coordpdb run000_prod.pdb PROH
coordpdb run000_memb.pdb MEMB
coordpdb run000_tip3.pdb WATB
coordpdb run000_pot.pdb POTB
coordpdb run000_cla.pdb CLAB

writepsf ab.xplor.psf
writepdb ab.pdb

You can find the log and script here:

Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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