Re: [AMBER] Running tleap with old prmtop

From: Samuel Bowerman <>
Date: Thu, 11 Aug 2016 12:30:18 -0500

Hi Taylor,

If you have the prmtop and the final frame from the NPT simulation, why not
just re-initialize from the solvated .rst7 file in the NVT from there? It
is not apparent to me why you would need to re-solvate everything if you
still have your simulation files. The type of ensemble is controlled by
the mdin file you supply pmemd/sander; it is not a property of the
prmtop/inpcrd. The only time I would re-solvate a system is if the
molecule rearranged significantly such that my original solvent environment
is now "too small."

Take care,
Samuel Bowerman
Ph.D. Candidate
Department of Physics
Illinois Institute of Technology

On Thu, Aug 11, 2016 at 12:13 PM, Taylor Quinn <> wrote:

> Hello,
> After running a long NPT MD simulation of a protein, I need to rerun the
> simulation in the NVT ensemble and thus need to resolvate the protein. Is
> there a simple way to resolvate a protein in tleap from a pdb of the last
> frame without making a new prmtop file/loading the different forcefields
> etc given that I have the old prmtop file? Basically, can I load a pdb,
> solvate it, and save an inpcrd/rst file to use with the prmtop file I have
> already? I was unsure if tleap has a command for that and couldn't find
> anything in the manual about it (I'm using Amber14).
> Best,
> --
> Taylor R Quinn
> Graduate Student, Wiest Lab
> University of Notre Dame
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Received on Thu Aug 11 2016 - 11:00:02 PDT
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