Re: [AMBER] ligand topology genaration

From: neha chaudhary <nehachaudhary769.gmail.com>
Date: Thu, 7 Jan 2016 11:03:36 +0530

Hi,

Thanks for replying. I have done MD simulations of protein-ligand complex
in Gromacs earlier now I want to convert the output files into Amber
format. I am trying to generate .prmtop files for protein, ligand and
protein-ligand complex. I am attaching input pdb files of protein, ligand
and protein-ligand complex herewith.

Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Jan 6, 2016 at 5:54 PM, Jason Swails <jason.swails.gmail.com> wrote:

> On Wed, Jan 6, 2016 at 4:25 AM, neha chaudhary <nehachaudhary769.gmail.com
> >
> wrote:
>
> > Hi,
> >
> > Thanks for replying. Actually I want to prepare topology files for
> protein,
> > ligand and protein-ligand complex. I used leaprc.ff99SB parameter file
> > earlier. I tried with leaprc.gaff parameter files also but I am still
> > getting errors. Please help.
> >
>
> ‚ÄčAs we said before, your original question lacked enough details to provide
> any more help than we already have. We'll need to know exactly what you've
> done (with exact input and output) to prepare the system and run it through
> leap in order to provide more targeted help.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Wed Jan 06 2016 - 22:00:04 PST
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