Hello Sir,
I have used gromacs for protein-ligand simulation. then I extracted
protein-ligand complex from rest of the system. Now I want to generate
amber topology file (.inpcrd) file for the protein-ligand complex.
What should I do for this?
Best Regards,
*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,
On Sun, Apr 26, 2015 at 2:03 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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 Sun Apr 26 2015 - 22:00:03 PDT
