AMBER Archive (2008)

Subject: Re: AMBER: Force field equation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Aug 21 2008 - 07:21:55 CDT

it's still confusing- you want to apply two sets of parameters at the
same time to the same bond/etc? would that make sense? you can use
more than one parameter for dihedrals, but I don't think it works for
bonds and angles, they can have only a single harmonic term.

On Thu, Aug 21, 2008 at 1:16 AM, Chih-Ying Lin <chihying_at_usc.edu> wrote:
>
>
> Yes, I am trying to mix force field components for different parts of my system.
> my second question is if possible , more sets of FF parameters to describe one bond / one angle/ one dihedral.
> in the frcmod file, we could only write one row of FF for one bond, one row of FF for one angle, and one row of FF for one dihedral.
>
> Is it possible for writing several rows for one bond/ one angle/ one dihedral?
>
> Thank you
> Lin
>
>
> ----- Original Message -----
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> Date: Wednesday, August 20, 2008 10:56 am
> Subject: Re: AMBER: Force field equation
> To: amber_at_scripps.edu
>
>> I don't know of gromos input files for AMber, but much recent work has
>> shown the Amber ff99SB force field for proteins to be superior to
>> gromos96. I would try to use ff99SB if possible, especially since it
>> is well tested with the amber codes.
>> your second question is not very clear, can you explain more about
>> what you want to do? are you trying to mix force field components for
>> different parts of your system?
>>
>> On Wed, Aug 20, 2008 at 12:05 PM, Chih-Ying Lin <chihying_at_usc.edu>
>> wrote:>
>> > Hi
>> > I know the force field (FF) parameters from Amber can port to
>> Gromacs.>
>> > But, could anyone know if Gromos 96 could port to Amber?
>> >
>> >
>> > In Amber, one set of FF parameters determine one bond/ one angle/
>> one dihedral.
>> > Could I use more sets of FF parameters to describe one bond /
>> one angle/ one dihedral?
>> >
>> > If so, please tell me how to do so.
>> >
>> > Thanks
>> > Lin
>> > ------------------------------------------------------------------
>> -----
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>>
>>
>>
>> --
>> ===================================================================
>> Carlos L. Simmerling, Ph.D.
>> Associate Professor Phone: (631) 632-1336
>> Center for Structural Biology Fax: (631) 632-1555
>> CMM Bldg, Room G80
>> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
>> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>> ===================================================================
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
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