On Wed, Feb 23, 2011 at 6:37 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> So it looks like it is a polarization factor - from the tutorial by
> Ross Walker on parametrizing a novel residue he omits any value here
> so for ordinary MD simulation the polarization effects are omitted?
>
Yes. Amber's polariz(s)able force field is amoeba, so these parameters have
no meaning outside of that context. You can find the full format
specification of *most* amber files at
http://ambermd.org/formats.html.
This includes the parameter files, prmtop files, etc.
Hope this helps,
Jason
> On Wed, Feb 23, 2011 at 8:14 AM, Jorgen Simonsen <jorgen589.gmail.com>
> wrote:
> > Hi all,
> >
> > I have parametrized a new residue and needed to change the naming of
> > some of the atoms in the lib file so I am add the missing parameters.
> > I am not quite sure where to find the "nonbonding" interaction terms.
> > The residue I am trying to parametrize is a modified water molecule
> > and in the parm99.dat file I find the following parameters for TIP3P
> >
> > MOD4 RE
> > .......
> >
> > OW 1.7683 0.1520 TIP3P water model
> > HW 0.0000 0.0000 TIP3P water model
> >
> > What is the MOD4 and RE section?
> >
> > The first part second column
> >
> > PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> > C 12.01 0.616 ! sp2 C carbonyl group
> > CA 12.01 0.360 sp2 C pure aromatic (benzene)
> >
> > what does the second column mean?
> >
> >
> > Thanks,
> >
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Feb 23 2011 - 06:00:05 PST
