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

From: Dr. Andreas W. Goetz <>
Date: Tue, 9 Aug 2016 15:39:00 -0700

> On Aug 9, 2016, at 1:26 PM, Fabrício Bracht <> wrote:
> In the second scenario, since my protein has loads of very mobile
> structures, it would be best to place a layer of solvent all around it as
> well as around the substrate for the reaction I pretend to simulate. This
> can easily be done with the solvateshell command in tleap, but, since
> solvateshell does not add the half-harmonic potentials in the prmtop file,
> I would then have to specify not only an fcap in the mdin file but also
> ivcap = 1, cutcap = "the size of cap I want" and xcap, ycap, zcap values as
> well.
> Is that correct?
> Isn't there a better way to do it? I think I am over complicating stuff

Use the solvatecap command (not solvateshell). It adds the information on the half-harmonic potential to the prmtop file. No additional information is required in the mdin file. I just tested it with Amber16, small water droplet at 500K, no water evaporates. You will see non-zero values in the RESTRAINT field of mdout.

All the best,

> 2016-08-09 16:27 GMT-03:00 David A Case <>:
>> 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?
>> No.
>>> 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.
>> ...dac
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Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771

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Received on Tue Aug 09 2016 - 16:00:02 PDT
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