AMBER Archive (2009)

Subject: RE: [AMBER] Using AMBER force fields in NAMD

From: Ross Walker (
Date: Tue Apr 28 2009 - 17:17:06 CDT

Hi Michael,

> I wish to use the AMBER98 force field for some MD studies, but already
> have
> code written to run my molecules in NAMD. I have been using CHARM22
> force
> field and topology files so far. I know NAMD will use AMBER force
> fields if
> setup properly, but I cannot find the AMBER98 topology file. I have
> downloaded 'amber10.ffparms.tar.bz2' and in the 'parm' folder found
> 'parm98.dat' which looks like the force field parameters. Do any of
> you
> know how to generate or where to find the proper topology file for
> Or, if it is needed when using AMBER forces?

There is no AMBER98 force field as far as I know, so I do not know what the
origin of parm98.dat is. Either way I would NOT use it. As far as I can see
it is parm94 with extra points added and some changes to (OH)OS-CT-CT-OS(OH)
terms. Note you should probably be using FF99SB which is parm99.dat with the
ff99SB frcmod applied. In NAMD it is very important that you set the 1-4
electrostatic divisor to 1.2 and the 1-4 VDW divisor to 2.0 (by default they
are 1.0). You should also probably check that the electrostatic constant is
set correctly - this may require editing the code and recompiling. This
should be (18.2223^2). I believe NAMD uses 332.0636 got this value.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
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