On Thu, Mar 25, 2010 at 10:55 PM, Palanimuthu M <palanibioinfo.gmail.com> wrote:
> Dear sir
>
> i referred the tutorials, in this am having some doubts sir. By
> using antechamber we are creating the library file, as well as the prmtop
> and inpcrd files for ligand. My protein is consist of the number of ligand
> molecule, how to rename these all ligands.
http://ambermd.org/tutorials/basic/tutorial4b/
That tutorial outlines exactly what you're asking here. Once you have
the prmtop, then the force field for your system is defined and it may
be used for simulations.
Do not rename all ligands. Do not forget that most proteins have
multiple Alanines, and the user does not have to rename each
alanine... In fact, to use your library file, you should keep all
names for residues of that ligand the same.
>
> *And then how to mix the traditional AMBER force fields with GAFF,*
They were designed to be compatible. The tutorial above does just this.
>
>
>
>
>
> On Fri, Mar 26, 2010 at 10:54 AM, manoj singh <mks.amber.gmail.com> wrote:
>
>> please refer to
>>
>> www.ambermd.org/tutorials
>>
>>
>> On Fri, Mar 26, 2010 at 1:23 AM, Palanimuthu M <palanibioinfo.gmail.com
>> >wrote:
>>
>> > Dear amber users
>> > how to create the topology file for protein ligand complex...
>> > _______________________________________________
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>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Mar 25 2010 - 23:30:04 PDT
