Re: [AMBER] Metal parametrization problem!!

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 1 Aug 2014 15:27:07 -0400

On Fri, Aug 1, 2014 at 2:38 PM, Pedro A. Baldera Aguayo <
a.baldera7.gmail.com> wrote:

> Yes, I did. However, I am facing problems with the wster molecules, and I
> do not how to deal with them.
>

‚ÄčIf the water molecules are part of the metal complex, then I think that
MCPB should have added the necessary hydrogens in one of the steps (or at
least there was a step to do so, if I recall correctly).

If it's just a "typical" water molecule that is part of the bulk solvent
(or exchanges with the bulk solvent), then tleap should add those
automatically, assuming that the water residue is named correctly.

Since I'm not super familiar with MCPB, I'll let Pengfei provide more
detailed answers if they're needed.

Good luck,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 01 2014 - 12:30:02 PDT
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