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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Received on Tue Sep 06 2011 - 02:30:02 PDT
