So. Just to see if I got things right. In my case, what I originally
intended was to perform qm/mm with gaussian. There are two main
possibilities for a simulation like that. An NVT simulation with a cutoff
value that would result in a discontinuity in the potential and all sorts
of problems as water molecules enter and exit this cutoff. A "water drop"
simulation in which I place my solute inside a solvent cap and set a cutoff
larger than my entire solute and water molecules.
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
here.
Thank you
Fabrício
2016-08-09 16:27 GMT-03:00 David A Case <david.case.rutgers.edu>:
> 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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Received on Tue Aug 09 2016 - 13:30:02 PDT
