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 Mon Sep 05 2011 - 16:30:05 PDT
