From: EPF \(Esben Peter Friis\) (EPF_at_novozymes.com)
Date: Mon Nov 01 2004 - 15:21:08 CST
I don't have access to my company's external web server, so I have put
the scripts on a private server at this rather obscure location:
I have also put them on the NAMD wiki, under NamdAndCHARMM:
There are two Python scripts:
charmm2namd which converts the CHARMM .psf file to a NAMD (XPLOR)
compatible one. This requires a conversion table between potential names
and numbers, which are found in MASS entries in CHARMM .rtf files.
Usually in the file MASSES.RTF from the desired CHARMM force field.
crd2pdb which (obviously :-) converts the CHARMM .crd coordinate file
into a .pdb file for use with NAMD. It does support removal of chainid
if the number of residues exceeds 10000 - eg with large water boxes, but
this has only been tried briefly, so beware.
It is strognly recommended to convert the CHARMM psf/crd pair into a
NAMD psf/pdb pair by using both scripts. Attempts to build the pdb file
in other ways often fail, as the atoms are not always listed in the same
Both scripts give a short help message if invoked without arguments.
From: Fred Salsbury [mailto:salsbufr_at_wfu.edu]
Sent: 1. november 2004 17:50
To: EPF (Esben Peter Friis)
Subject: xplor to charmm
On the namd mailing list, I read that you had a script to convert a
charmm psf file into a namd-usable psf file? Could I use it?
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