AMBER Archive (2008)

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

From: Alan (alanwilter_at_gmail.com)
Date: Fri Aug 29 2008 - 04:00:01 CDT

Thank you Ilyas because this what I was thinking too before sending my doubt
to this list. In the end what they answer to me is OK to solve my problem
and I do second you in this point.
Cheers,
Alan

On Thu, Aug 28, 2008 at 10:58 PM, Ilyas Yildirim <yildirim_at_pas.rochester.edu
> wrote:

> > 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
>
> Ross, I thought the way frcmod works is as follows: If you define any
> dihedrals in the frcmod file, it will first remove all the entries from
> the previously defined force field and add the new entries to leap. Let's
> say that my xleap commands are like this:
>
> ---- xleap.in -----
> source leaprc.rna.ff99
> loadamberparams frcmod
> -------------------
>
> and let's say my frcmod file is as follows:
>
> ----- frcmod -----
> Modified dihedral parameters
> MASS
>
> BOND
>
> ANGL
>
> DIHE
> OS-CT-N*-CK 1 5.00 000.0 2. parm98,
> IMPR
>
> NONB
> ------------------
>
> What this will do is, it will remove any entries defined for OS-CT-N*-CK
> and only add this particular dihedral parameter. This means that in the
> prmtop file, there will be only 1 parameter set defined for this
> particular dihedral. In the amber99.dat file, there are 2 sets defined for
> this particular dihedral (2 periodicities).
>
> OS-CT-N*-CK 1 0.00 000.0 -2. parm98,
> OS-CT-N*-CK 1 2.50 0.0 1. parm98,
>
> So, having the above frcmod file will remove the above entries and add
> parameters for the periodicity n=2 only. I just double checked this
> using rdparm. So, I dont think that there is any reason to define zero
> parameters for the unwanted entries (except that if someone is doing TI
> calculation and have this particular entry nonzero).
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> = Department of Physics - =
> = University of Rochester - =
> = 585-275-6766 (office) - 585-267-5644 (home) =
> = http://www.pas.rochester.edu/~yildirim/ =
> ---------------------------------------------------------------
>
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-- 
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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