Re: Generate psf file in x-plor format

From: Vermaas, Joshua (
Date: Thu Nov 17 2016 - 09:47:42 CST

Hi Nehad,

Does it have numbers for atomtypes (third column of the psf)? If so, its
in charmm format. If it has alphanumeric atomtypes, its in xplor format.
Where did your rtf file come from? I didn't know the Amber folks
distributed their force field in a CHARMM-compatible way. If its not
written in the standard way for CHARMM topology files, psfgen will
happily put what it sees as the atomtypes (which might be numbers) in
the type field, and give you the error that you see.


On 11/17/2016 05:09 AM, Nehad Elsalamouny wrote:
> Dear NAMD users,
> I want to prepare my protein for NAMD in amber format. I generated a psf file for the protein using amber ff (topology file used is parm14sb_all.rtf) using the following script:
> package require psfgen
> topology parm14sb_all.rtf
> pdbalias residue HIS HIP
> pdbalias atom ILE CD1 CD
> segment A {pdb xxxxp.pdb}
> patch DISU A:42 A:58
> patch DISU A:50 A:111
> patch DISU A:136 A:201
> patch DISU A:168 A:182
> patch DISU A:191 A:220
> coordpdb xxxxp.pdb A
> guesscoord
> writepdb xxxx.pdb
> writepsf xxxx.psf
> exit
> When I try to solvate the protein:
> package require solvate
> solvate xxxx.psf xxxx.pdb -t 5 -o xxxx-wb
> I get an error message: unable to open psf file. File is in charmm format should be in x-plor.
> However I can see the file is in x-plor format!
> Can you help me solve this problem please?
> Thanks,
> Nehad

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