Using Amber FF in NAMD

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Mar 18 2009 - 18:13:33 CDT

I am attempting to use one of the amber force field parameter sets in
namd, and am getting the error:

Info: Using AMBER format force field!
Info: AMBER PARM FILE ../parm98.dat
Info: COORDINATE PDB ../xxx_ionized.pdb
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Reading parm file (../parm98.dat) ...
FATAL ERROR: Failed to read AMBER parm file!

I am using parm98.dat found in the distribution available at:
http://ambermd.org/dbase.html

The namd UG says that namd should be able to read parm files in
either the Amber 6 or 7 format, although it was unclear to me if
there has been another change in the format between Amber 7 and the
most recent distribution. If anyone has a suggestion or could point
me to versions of the force fields (parm98 or parm94 and ff98sb), I
would appreciate it.

Also, the UG says that, " If amber is set to on, then parmfile must
be defined, and structure and parameters should not be defined." If
you are using a pdb file for the coordinates, how does namd deal with
not having a psf or similar topology file. as is required in a
standard run with the charmm force field?

Josh

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