Dear James,
> As I understood this server may generate topology for the big molecule with
> the non-standart residues for the amber-like force fields.
R.E.D. & R.E.D. Server generate force field (FF) library(ies) for a
non-standard residue. These FF libs are then loaded in LEaP and used
in association with existing FF libs to generate prmtop/prmcrd files.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
or
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
> Could you tell me what additions modifications are needed for REDs output
> to obtain GROMACS .top file ?
See
http://ffamber.cnsm.csulb.edu/
We are about to submit a paper about this topic...
regards, Francois
> 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
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Received on Tue Jan 31 2012 - 00:00:02 PST
