Re: [AMBER] ligand topology genaration

From: Jason Swails <>
Date: Thu, 7 Jan 2016 06:52:05 -0500

On Thu, Jan 7, 2016 at 12:33 AM, neha chaudhary <>

> 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.

​We still need to know the exact commands you were using, as well as the
exact error messages you were receiving when trying those commands.
Otherwise we have to guess, which is more often than not a waste of time.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 07 2016 - 04:00:03 PST
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