AMBER Archive (2008)

Subject: Re: AMBER: question - gaff and leaprc.ff03ua

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Sun Nov 23 2008 - 10:43:48 CST

Dear  All,

I want to ask if I can use leaprc.ff03ua force field directly in leap ( not doing any operations like evaluating charges or generating a prepin or mol2 file ) for my n-alkanes simulations ? If not , Could you give me the information about that? And I also searched the Literature , but I couldnąt find any study about  leaprc.ff03ua . So , Could you suggest some referance studies that include ff03ua force field ?
Kind regards,

--- On Wed, 11/19/08, David A. Case <case_at_biomaps.rutgers.edu> wrote:

From: David A. Case <case_at_biomaps.rutgers.edu>
Subject: Re: AMBER: question - gaff and leaprc.ff03ua
To: amber_at_scripps.edu
Date: Wednesday, November 19, 2008, 9:08 AM

On Wed, Nov 19, 2008, oguz gurbulak wrote:
>
> I want to do a geometric optimization in order to find the new xyz
> cordinates of my molecule and after that evaluate the partial charges of
> my molecule before using gaff or leaprc.ff03ua in xleap . Is ?t necessary
> to do all these operations when using gaff or leaprc.ff03ua ?

Depends. It's always a good idea to have a good structure to start with,
so
geometry optimization should not hurt. The bcc charge scheme will
automatically optimize the geometry (at the AM1 level), so you don't
strictly
need to do it yourself. If you are looking for RESP charges, you will surely
need an optimized geometry.

...dac

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