Re: [AMBER] Recover the water model and periodic box from built parm files

From: Brian Radak <>
Date: Mon, 22 Jun 2015 10:44:06 -0500

If I understand your purpose correctly, you should be able to recover a
PDB file of the system using ambpdb and then reload the whole thing into
tleap. This would preserve a representative configuration as well as the
overall atom count.

I should note, this is not usually done and would require inserting a
"TER" character after /every single water molecule/ion/ in the PDB file
(a simple awk script can do this pretty easily). You can then re-assign
the box parameters manually in tleap (use "set box" instead of
"solvatebox" or "solvateoct").

As per Jason's remarks, you can't directly extract the lib and frcmod
information, but I would assume you have some idea as to what these are.
In any event you can trial/error use multiple force fields and then
compare parameters directly using ParmEd until you have what you want (I
forget the command, "printInfo" maybe? It's pretty fantastic).


On 06/22/2015 09:12 AM, Jason Swails wrote:
> On Mon, 2015-06-22 at 14:01 +0000, Yin, Xing wrote:
>> Dear Developers and Users,
>> I'm trying to repeat the calculation of an Amber model with some
>> modifications. However I only have the built .prmtop and .inpcrd
>> files. The colleague who made the model solvated the model manually
>> in
>> tleap and there is no script left. Is there a way to recover the
>> arguments used. The periodic box should be a truncated octahedron by
>> looking at the final model.
> No there's not. And even if you could, it wouldn't produce the exact
> same results unless you had the original starting structure (since there
> would be a different number of waters surrounding the system).
> At the end of the day, this shouldn't matter, though.
> HTH,
> Jason

Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
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Received on Mon Jun 22 2015 - 09:00:02 PDT
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