[gmx-users] Comparing two Ptn-Ptn docking models

[Diogo Martins de Sá]

Thanks for the advice Justin!

I'm looking in to it right now.

My box has the following dimensions:
9.10300  12.10200  11.46200

How would you define "continuous pull", is it pull in which the distance
increases indefinitely but slow enough not to trespass the distance
limits/conditions? I get the part where the periodic images can't
interact and the "less than one half the length of the box" condition.
But how do I know if my box and my system are apt for umbrella sampling?
will I be able to use mdrun -rerun with my current system?


best regards

Diogo



From: Justin Lemkul <jalemkul at ...>
Subject: Re: [gmx-users] Comparing two Ptn-Ptn docking models
Newsgroups: gmane.science.biology.gromacs.user
Date: 2015-03-11 01:36:06 GMT (1 hour and 10 minutes ago)


On 3/10/15 9:34 PM, Diogo Martins de Sá wrote:
> Hi all,
>
>
> I have two proteins which I've docked and obtained two models, dock1 and
> dock2. Both corroborate, to some point, with literature experiments.
>
>
> I ran both models in a 76ns simulation, using 43a1 force field and PME.
>
>
> I have managed to map all salt bridges and their distances through the
> simulation (the intermolecular ones! between ARG, LYS, ASP and GLU), all
> hydrogen bonds and their percentage of appearance during the simulation
> (using one of Justin's scripts), and I also have all other contacts
> made between atoms and managed to make index group for all these stuff.
>
>
> In the .mdp I have specified Protein and Protein2 as energygroups.
>
>
>
> I have some ideas but I would like to know what would you guys recommend
> I do to infer which of the two models is most likely to be correct. What
> useful calculations should I look for? What energy terms (just Short
> range ones?)
>
>
> I guess the best thing to look for would be free energy of binding...
> I've been reading about it and came upon David Mobley and Justin's
> tutorial, which seem to work using PME (links at the end)
> When running the MDS of the ligand (in my case, also a protein) in
> water, should I start from scratch? Or can I use tbpconv to extract just
> the ligand out of my .tpr and then call mdrun -rerun with the new tpr
> and new coupling parameters? Would that satisfy any of the two
> tutorials?
>

Don't do an alchemical transformation with a protein. Convergence is
all but 
hopeless. What you want is a PMF with umbrella sampling (I also have a
tutorial 
for that).

-Justin

> thanks in advance
> Diogo
>
> Justin tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy_old/index.html
>
> Mobley's:
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
>
>
>
> Thanks in advance,
>
> Diogo
>

-- 
==================================================

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 ... | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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