Hi Jason,
I've already heard many about RED previously.
As I understood this server may generate topology for the big molecule with
the non-standart residues for the amber-like force fields.
Could you tell me what additions modifications are needed for REDs output
to obtain GROMACS .top file ?
James
2012/1/30 Jason Swails <jason.swails.gmail.com>
> On Sun, Jan 29, 2012 at 12:12 PM, James Starlight <jmsstarlight.gmail.com
> >wrote:
>
> > Dear Amber Users!
> >
> >
> > I want to prepare my PDB wich contain some non-standart residues for
> > the simulation in the GROMACS in Amber99 force field.
> >
>
> I'm skeptical that you really want to use the Amber 99 force field. That
> force field is 13 years old with well-known deficiencies, so unless you
> have a specific (good) reason for using it, I would strongly suggest a more
> modern force field like ff99SB.
>
>
> > I've found that Antechamber software wich is prt of amber tools would
> > be best way to prepart .ITP topology file suitable for the Gromacs
> > simulation.
> >
>
> Antechamber just calculates partial charges and such for custom residues,
> and it assigns atom types for the generalized amber force field (gaff) for
> these molecules. This is primarily designed to parametrize small organic
> compounds that will work seamlessly with the other Amber force fields. If
> you have residue fragments or more complex residues to derive charges for,
> I would suggest a more appropriate tool, like R.E.D. Server or something
> similar.
>
>
> > Could you tell me where I could find some tutorial about such topology
> > preparation ?
> >
>
> All of the available Amber tutorials are found at
> http://ambermd.org/tutorials/
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Jan 30 2012 - 22:30:03 PST
