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

From: David A Case <>
Date: Mon, 22 Jun 2015 13:17:26 -0400

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


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Received on Mon Jun 22 2015 - 10:30:02 PDT
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