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

From: Brian Radak <>
Date: Mon, 22 Jun 2015 15:34:03 -0500

Ah, no, I'm not sure - that's just how I recall doing things from a few
years back. I can only say that I know that /that/ worked and it wasn't
too much of an ordeal to get going. It's very possible that an older and
wiser Brian would find things are a bit more simple.


On 06/22/2015 12:17 PM, David A Case wrote:
> On Mon, Jun 22, 2015, Brian Radak wrote:
>> 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
> Are you you sure this is needed? We read waters from RCSB pdb files fine, and
> they don't have TER cards between waters. In general, any file that comes out
> of ambpdb ought to be acceptable as input to tleap (without hand-editing).
> Exceptions to this rule should be brought to our attention, as they represent
> bugs.
> ....dac
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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 - 14:00:03 PDT
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