AMBER Archive (2008)

Subject: Re: AMBER: to understand how frcmod.ff99SB works

From: Alan (alanwilter_at_gmail.com)
Date: Thu Aug 28 2008 - 13:36:55 CDT

Melinda and Ross, thanks a lot!
Alan

On Thu, Aug 28, 2008 at 5:59 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Alan,
>
>
>
> Amber allows multiple dihedrals but only if the periodicity is different
> for each dihedral. So in the case below the -4 and -3 periodicity entries
> are added as additional dihedrals while the -2 and 1 entries in
> frcmod.ff99SB should overwrite the existing two entries from parm99.dat.
>
>
>
> Loading any additional parameters with the same atom types and matching
> periodicities will overwrite existing entries already loaded that match that
> atom type set and periodicity. Hence why FF99SB has
>
>
>
> C -N -CT-C 1 0.00 0.0 1.
>
>
>
> This is equivalent of deleting the original 0.8 barrier height dihedral
> from parm99.dat.
>
>
>
> I hope this helps,
>
> Ross
>
>
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Alan
> *Sent:* Thursday, August 28, 2008 3:29 AM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: to understand how frcmod.ff99SB works
>
>
>
> Dears,
>
>
>
> So, I would like to understand what exactly is happening to parameters when
> you load from frcmod.ff99SB.
>
>
>
> So in tleap, loading leaprc.ff99SB, it will first load parm99.dat and then
> frcmod.ff99SB. Taking a set o parameter to illustrate, we have in
> parm99.dat, DIHE:
>
>
>
> C -N -CT-C 1 0.850 180.000 -2.
>
> C -N -CT-C 1 0.800 0.000 1.
>
>
>
> Looking at frcmod.ff99SB, we have:
>
>
>
> C -N -CT-C 1 0.00 0.0 -4. four amplitudes
> and
>
> C -N -CT-C 1 0.42 0.0 -3. phases for phi
>
> C -N -CT-C 1 0.27 0.0 -2.
>
> C -N -CT-C 1 0.00 0.0 1.
>
>
>
> So what exactly is happening here? Are those 4 new entries added to the 2
> first original or the simply replacing them?
>
>
>
> Many thanks in advance.
>
>
>
> Cheers,
>
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
> 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

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