Re: [AMBER] many initial systems for a two molecules system

From: Fabian Glaser <>
Date: Mon, 8 Sep 2014 17:35:36 +0300

Oh I see, I thought to use the center of mass starting from a PDB structure....yes they are big molecules

Their flexibility is not so large since they have 3-4 aromatic rings, so you say I cannot use the RDF approach without previously equilibrating the system seriously?

Well, my original idea was to gain some insight at all about their interaction, couldn't I first run a single molecule and then freeze the best 5 conformations to calculate RDF?

Thanks a lot anyway...


Fabian Glaser, PhD

Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU

The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
Tel: +972 4 8293701
Fax: +972 4 8225153

On Sep 8, 2014, at 5:22 PM, Jason Swails <> wrote:

> On Sun, 2014-09-07 at 15:05 +0300, Fabian Glaser wrote:
>> Dear Jason,
>> Thanks again, more questions, hope this is OK ....
>> 1) If I understand correctly, what you suggest is to perform a
>> simulation with explicit water, with a number of molecules at a
>> certain fixed distance of a central molecule and compute the density
>> distribution of all of them around the central molecule after
>> simulation with RDF and PMF functions for the central molecule once
>> the simulation is completed. Correct? Or you mean just to use a number
>> of molecules in a box at the same distance between them?
> No, not a fixed distance. Just a bunch of the molecules in a simulation
> box that move freely. There is no "central" molecule (or alternatively,
> every molecule is a "central" molecule surrounded by all of the others).
>> 2) How to choose the distance to use between the central molecules and
>> the other molecules to create the water box? The molecules are about
>> 20 Ang long full extended, so I guess the box has to be about 50 Ang
>> minimum, I could take a distance of 12 Ang for any molecule is that a
>> good approach?
> I was under the impression that the molecules were significantly
> smaller. The whole RDF approach is unlikely to work with such a large
> molecule (especially if it is not rigid). It is going to be difficult
> to characterize the interactions between two large, flexible molecules
> since there are many degrees of freedom dictating the nature of their
> interactions (a simple distance is unlikely to give all the information
> you need unless you can fully sample the equilibrium distributions of
> their different conformational states -- akin to umbrella sampling).
>> 3) How many molecules to add, I have no idea what the concentration
>> should be in vivo? At which distance from the central molecule?
> This sounds like information you would need to figure out as part of
> your study. Since it's not my study, I don't know.
>> 4) How long the simulation should be? Until know I did 20 ns
>> simulations, but would that be enough to calculate the RDF function
>> later?
> In general, they should be long enough to converge your results. A
> decent first check is to compute the properties you're trying to find
> for separate chunks of your simulation and make sure that they are the
> same.
>> 5) Is the parametrization with antechamber a reasonable one?
> Depends on your molecule. For a flexible molecule that is ~20 A
> extended, I would not rely on antechamber torsion profiles being
> correct.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 08 2014 - 08:00:02 PDT
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