Re: Canīt use charmm to perform dcd analysis

From: Himanshu Khandelia (
Date: Mon May 21 2007 - 01:17:58 CDT


Charmm is less forgiving about the exact format of pdb and psf files. I
would recommend regenerating the psf in charmm and converting the
namd-generated pdb to a charmm .crd format file, or at least to a pdb
format which charmm can read (the column format is different)

You will run into problems if the residue numbering in your psf is not
continuous. Take a look at this example from the charmm forums

Himanshu Khandelia, PhD
Research Assistant Professor (Postdoc)
MEMPHYS, Center for Membrane Physics:
University of Southern Denmark (SDU)
Odense M 5230, Denmark

Phone: +4565503510

On Sun, 20 May 2007, Victor Capistr wrote:

> Hello
> We have performed a namd simulation using a pdb and a psf both generated
> with vmd. We havenÂīt been able to perform an
> analysis on the dcds using charmm due to our inability to read on charmm the
> pdb specified in namdÂīs configuration file.
> Is there a way to perform an analysis on charmm using those files?

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