PSF/top/inp for joint charmm/amber benchmark

From: Andrew Fant (
Date: Tue Mar 31 2009 - 17:03:48 CDT

Does anyone have a psf for methotrexate that they are willing to share
with me? I know that there is a topology pre-generated in the
commercial version of CHARMM, and that there is a "joint AMBER/CHARMM"
benchmark using what looks to be 3DFR from the pdb distributed with
amber 10, but my usual analysis tools are rather picky about demanding a
psf-formatted topology to go with a DCD formatted trajectory. I need to
generate some data for a demonstration, and the DHFR/MTX system is just
about the right size, but I need to include a small-molecule ligand, and
I don't have the time to parameterize from scratch with G*ussian. I've
been searching around with Google, and I find it hard to believe that
this is the first time that someone has wanted to simulate bound DHFR
with NAMD.

Thanks in advance for any help,

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