Re: [AMBER] Reference structure for targeted MD

From: Daniel Roe <>
Date: Tue, 16 May 2017 12:02:15 -0400


I've recently uploaded a script to GitHub that I've been using for a
while which is a wrapper around tleap for solvating with a specific
number of water molecules:

If you end up trying it I'd appreciate any feedback. Help and a simple
example are provided. As long as tleap and cpptraj are in your PATH
the script should work.


On Mon, May 15, 2017 at 10:26 PM, Francesco Gentile
<> wrote:
> Hello everyone,
> I am trying to run a targeted MD simulation. Reading the manual, it says
> that both the reference and the input coordinates should match the prmtop
> file. I am wondering how this can be done, as I don't expect to see the
> same number of water molecules by solvating the two structures, even using
> the same parameters for leap. Thanks in advance for your help,
> --
> Francesco Gentile
> PhD Candidate, Biophysics
> CCIS 3-215, Department of Physics
> 7-112, Li Ka Shing Centre for Health Research Innovation
> University of Alberta, Edmonton, AB T6G 2E1
> Canada
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue May 16 2017 - 09:30:02 PDT
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