Hi Astrid,
Thank you for the info.
But in addition to negative force constant, there are also some negative
multiplicity for GLYCAM dihedral parameters. So would these negative
multiplicities be a problem for amb2gmx as well?
Thanks,
Yun
On Tue, Sep 6, 2011 at 2:07 AM, Astrid Maaß <astrid.maass.scai.fraunhofer.de
> wrote:
> Hi Yun Shi,
>
>
> I used amb2gmx.pl some time ago and if I remember correctly, for torsions,
> amb2gmx.pl converts the Amber-cosine series in a
> Ryckaert-Bellemans-potential. This was OK in most of the cases, but when
> amb2gmx.pl encounters a negative force constant it may not translate the
> potential correctly. I do not know, whether this behavior has been fixed in
> the meantime, but you could bypass it by using a phase shift of 180 instead
> of a negative sign in the force constant for the respective term. You might
> use rdparm to check whether this difficulty would apply to your system
> anyways.
>
> Hope that helps
> Astrid
>
>
>
>
> ----- Ursprüngliche Mail -----
> Von: "Yun Shi" <yunshi09.gmail.com>
> An: "AMBER Mailing List" <amber.ambermd.org>
> Gesendet: Dienstag, 6. September 2011 01:22:19
> Betreff: Re: [AMBER] how to fill in missing parameters in tleap?
>
> Hi all,
>
> For this specific molecule, I wonder if it's possible to manually set
> parameters for the non-standard parts.
>
> I was thinking about using GLYCAM and amber99SB, while avoiding the use of
> GAFF force field, with the help of amb2gmx.pl and GROMACS software.
>
> 1. Set geometrical parameters and atomic charges to all standard residues
> using GLYCAM and 99SB.
>
> 2. Derive RESP charges for the modified TRP and thio-glycosidic linkage.
>
> 3. With GROMACS topology files, set geometrical parameters for the modified
> TRP and thio-glycosidic linkage according to 99SB. That is, define atom
> types, bonds (CT-S), angles (CT-S-CT, CT-CT-S), and dihedrals (X-CT-S-X)
> with corresponding parameters from 99SB. And for N, H, CA, CB, and indole
> parts of the modified TRP, just use whatever geometrical parameters from
> the
> standard TRP in 99SB.
>
> 4. Combine all these parts in GROMACS format.
>
>
> On Sun, Aug 28, 2011 at 6:12 AM, case <case.biomaps.rutgers.edu> wrote:
>
> > On Fri, Aug 26, 2011, Jason Swails wrote:
> > >
> > > Use parmchk. If you run the program with no arguments, it tells you
> how
> > to
> > > use it. By default, it will search gaff.dat and pull out reasonable
> > > parameters, dumping them to an frcmod file. If there's anything it
> > simply
> > > *can't* find, it will put a placeholder (all parameters are 0) and say
> > > "ATTN, need revision". You have to fix those parameters.
> >
> > Parmchk does a bit more than just look in gaff.dat: it estimates missing
> > parameters by several algorithms. In its default mode, parameters in
> > gaff.dat
> > are not put into the frcmod file; parameters it estimates on its own are
> > output; finally, things it can't figure out get placeholders.
> > >
> > > However, I would warn you that gaff dihedrals should not necessarily be
> > > accepted. Run short simulations to make sure they make sense, as you
> may
> > > have to modify some of them by hand.
> >
> > This is excellent advice.
> >
> > ...dac
> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Sep 06 2011 - 08:30:03 PDT
