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).
Cheers,
Brian
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
email: radak.uchicago.edu
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Received on Mon Jun 22 2015 - 09:00:02 PDT
