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 - 08:00:02 PST
