AMBER Archive (2009)

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

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Tue Apr 28 2009 - 17:23:15 CDT

parm98.dat is a modification of parm94 (ff94) with few changes for
dihedral angles related to puckering and chi angle for nucleic acids.
Nothing else. It uses the same topologies as parm94.

Piotr

On Tue, 28 Apr 2009, Ross Walker wrote:

> From: Ross Walker <ross_at_rosswalker.co.uk>
> Sender: amber-bounces_at_ambermd.org
> To: 'AMBER Mailing List' <amber_at_ambermd.org>
> Date: Tue, 28 Apr 2009 15:17:06 -0700
> Subject: RE: [AMBER] Using AMBER force fields in NAMD
> Reply-To: AMBER Mailing List <amber_at_ambermd.org>
>
> 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
>> NAMD?
>> 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,
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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