Amber ff99sb force-field in namd

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Mar 18 2009 - 17:25:13 CDT

A quick question for those who have experience using the Amber force
fields in NAMD. I want to use the 'Stony Brook' mod of ff99 (i.e.
ff99sb). I am not that familiar with Amber, but have read the section
of the NAMD user's guide that details how to modify the input file
for NAMD. The Amber FF distribution contains parm99.dat which is the
original ff99 force field. Amber appears to read a separate
modification, in this case frcmod,ff99SB, however namd only allows
for a single input.

frcmod.ff99SB only contains a couple of lines of data. For those who
have used modified versions of Amber FF's, have you simply merged the
two files, replacing the lines in parm99.dat with the appropriate
changes found in the frcmod file?

Thanks
Josh

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