Re: [AMBER] Question about usage of external QM in QM/MM

From: David A Case <>
Date: Tue, 9 Aug 2016 15:27:00 -0400

On Tue, Aug 09, 2016, Fabrício Bracht wrote:

> Does the solvateshell command in tleap work for what we've
> discussed? I mean does it create a cap around the solute with the
> restraining half-harmonic potential in the prmtop file?


> If I am actually supposer to use solvatecap from tleap, how do I pass a
> list of residues to solvatecap? I have tried:

Why do you want to pass a list of residues to solvatecap? To get the center
of mass of those residues to be the center of the cap? LEaP doesn't have a
syntax to specify a range of residues. You might want to use some other
program to compute the desired center of the cap, the enter those coordanates
as a list (surrounded by "{" and "}") into the solvatecap command.

Re the other email: you do have to specify fcap in the mdin file, at least
as I remember.


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Received on Tue Aug 09 2016 - 12:30:02 PDT
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