[gmx-developers] Intermolecular interactions

[Mark Abraham]

Hi,

The patch Justin mentions seems to work and is likely to be in 5.1

Mark

On Sun, Jun 14, 2015 at 4:04 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
> Hi Devs,
>
> I am working on doing some absolute binding free energy calculations and am
> running into difficulty preserving the orientation of the ligand.  I have
> tried
> a bunch of things to try to recapitulate the behavior we can achieve in
> CHARMM
> (e.g. dx.doi.org/10.1021/ci300505n) with intermolecular dihedral and angle
> restraints, but long story short, I haven't found a way to do it.  I need
> to
> preserve the dihedral between the centers-of-mass of four rings (two in a
> cofactor, two in the inhibitor being annihilated).  Merging the topologies
> didn't work because I can't selectively annihilate the inhibitor unless the
> cofactor is also annihilated, and use of explicit B-state dummy atom types
> for
> the inhibitor requires manual editing of hundreds of bonded interactions,
> which
> I don't think is effective.
>
> It seems that there is a patch in Gerrit that has languished for several
> months
> (https://gerrit.gromacs.org/#/c/2566/) that appears it might do what I
> need.
>
> I'm happy to provide feedback/testing on that patch if someone (Berk?) can
> tell
> me if I can use the intermolecular bondeds to set up a dihedral restraint
> that
> is lambda-dependent (i.e. perturbed as a function of restraint-lambdas in
> the
> .mdp)?  The pull code works fine to preserve a few translational
> restraints that
> I need, but the relative orientation is the issue I have.  Simply applying
> an
> intermolecular dihedral potential would likely also suffice in lieu of a
> restraint if the latter is not possible.
>
> Getting this feature implemented would be a great benefit and I'm happy to
> be
> the guinea pig for it to get it merged.
>
> Thanks for any insight!
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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