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

From: Yin, Xing <>
Date: Tue, 23 Jun 2015 14:04:17 +0000

Dear all,

I removed all the water molecules and re-solvate in LEaP and it seems to work fine. Thanks very much! :)

Best wishes,

On 06/22/2015 04:52 PM, Jason Swails wrote:
> On Mon, Jun 22, 2015 at 4:34 PM, Brian Radak <>
> wrote:
>> 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.
> ​From a functional perspective, TER cards are only needed by LEaP to
> *prevent* adjacent residues from being linked. The only time LEaP ever
> does this is when that residue has a HEAD or TAIL defined (which it
> obviously doesn't for water).
> So it's necessary between protein or nucleic acid chains, but not after
> isolated molecules. As with Dave, I've never had problems using
> ambpdb-generated files directly with tleap.
> HTH,
> Jason
> ​
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Received on Tue Jun 23 2015 - 07:30:02 PDT
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