On Sat, Apr 25, 2015 at 4:46 AM, neha chaudhary <nehachaudhary769.gmail.com>
wrote:
> Hi,
>
> Yes sir, you guessed right. But sir I want amber output files for
> protein-ligand complex. As you suggested, ligand's topology is generated
> after extraction but with protein it is showing error.
As I said in my last email, when you provide no details about what you did
and what happened, it is *much* harder for us to help.
> Also suggest how to
> again merge output files of ligand and protein after conversion to get a
> combined .prmtop file for complex.
>
Did you work through any of the tutorials on
http://ambermd.org/tutorials/
like I suggested? Particularly
http://ambermd.org/tutorials/basic/tutorial4b/? That tutorial walks
through the exact procedure needed to parametrize a non-covalent ligand
bound in a protein in a PDB file. Work through that tutorial, make sure
you understand what is happening, and then apply the same approach to your
problem.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Apr 25 2015 - 14:00:02 PDT
