Re: Amber ff99sb force-field in namd

From: Benjamin Bouvier (benjamin.bouvier_at_ibcp.fr)
Date: Wed Mar 18 2009 - 18:19:23 CDT

Josh,

What NAMD reads is the AMBER topology file -- a subset of the chosen force
field that describes your particular system. It already explicitely
contains all the parameters for your system, so NAMD does not need to know
what forcefield was actually used to generate it (eg, parm99.dat).
The choice of the force field is done during the generation of the
topology file, usually with the Amber tools tleap or xleap. Typically
you'll want to load the ff99 force field, patch it to ff99sb, and load
your structure to generate the topology, which you can then use in NAMD.

Tleap and xleap are available for free in the Amber Tools, and tutorials
about how to use them can be found on the web (eg,
http://ambermd.org/tutorial/)
Hope this helps,

Benjamin

On Wed, 18 Mar 2009 23:25:13 +0100, Joshua Adelman <jadelman_at_berkeley.edu>
wrote:

> 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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