Re: [AMBER] MD simulation for multiple ligands

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 23 Nov 2015 17:28:50 -0500

On Mon, Nov 23, 2015 at 10:57 AM, Balajee Ramachandran <
rbalajeebio.gmail.com> wrote:

> Dear members,
>
> I would like to perform MD simulation for one protein with multiple ligands
> (for eg., 3 ligands). Please let me know the procedure to prepare the
> ligands to execute.
>

‚ÄčThe same way you do it for one ligand. See tutorial B4 at
http://ambermd.org/tutorials for a demonstration

You need to run antechamber once for each *kind* of ligand you have (if all
3 ligands are the same molecule, you only have to run antechamber once, but
if they are different you have to run antechamber 3 times on each of the 3
individual ligand molecules).

‚ÄčThen just make sure you load all of the ligand library files you created
(or if all ligands are the same, just load the one you created), along with
each of the frcmod files you generated with parmchk2.

Good luck,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 23 2015 - 14:30:07 PST
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