From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Jul 05 2016 - 18:28:59 CDT
Every problem is unique, so unfortunately I don’t have more specific advice to give. A higher stratification may work for you, but also try to determine why the energy is so high, e.g., does the protein begin to unfold during extraction?
Best,
JC
> On Jul 1, 2016, at 5:13 PM, Gabriel Jara <gabriel.fcq.unc.ar_at_gmail.com> wrote:
>
> Hi Gumbart,
>
> Thank you for the answer. Now, I understand that the convergence is slow, so I focued in the stratification strategy in order to improve the results, do u have any tips to this issue?
>
> I looked at the tutorial, but I am not sure if it is what I looking for, because I am intereted in a PMF profile more than of the total variation of free energy.
>
> Thank again.
>
> Gabriel
>
>
> On Thu, Jun 30, 2016 at 5:51 PM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
> Hi Gabriel,
>
> I would suggest taking a look at the following tutorial and associated papers: http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf <http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf>
>
> Calculating a binding free energy can be very challenging! Particularly for a flexible ligand like ATP. And, to be honest, ABF has a great tendency to produce values that are far too high initially (due to non-equilibrium effects), then requiring potentially hundreds of ns to come back down.
>
> Best,
> JC
>
>> On Jun 30, 2016, at 2:25 PM, Gabriel Jara <gabriel.fcq.unc.ar_at_gmail.com <mailto:gabriel.fcq.unc.ar_at_gmail.com>> wrote:
>>
>> Dear all,
>>
>> I am interested in studying the process and free energy of binding of ATP to the active site and coordinated to a magnesium. The strategy I thought was to start from the protein:ligand complex and to perform ABF simulations in order to calculate the PMF of unbinding and in this way to describe the mechanism of binding and its free energy.
>>
>> The problem is that I obtained huge free-energy values, ~150 kcal/mol with simulation of 80 ns. I tested different reaction coordinates, but the results are similar. At the moment, I am testing a open-conformation of the protein, in order to know the conformational effect.
>>
>> The reaction coordinate selected is a distance between the center of mass of the whole ligand or the nitrogenenous base or the phosphate, and a non-flexible loop in the active site. In addition, the magnesium is released from the active site along with ATP, only if I explicitly add it in the reaction coordinate.
>>
>> I have little experience about ABF, and I would like to know tips to overcome this issue.
>>
>> Following attached the collective variable file
>>
>>
>> Colvarstrajfrequency 1000
>> Colvarsrestartfrequency 1000
>> colvar {
>> name COMDistance
>> width 0.1
>> lowerboundary 7.00
>> upperboundary 20.00
>> lowerwallconstant 10.0
>> upperwallconstant 10.0
>> distance {
>> group1 {
>> atomnumbers { 22 23 24 25 26 27 28 29 30 31 32 33 34 35 }
>> }
>> group2 {
>> atomnumbers { 5461 5462 5463 5464 5471 5472 5473 5474 5475 5476 5492 5493 5494 5495 5496 5497 5504 5505 }
>> }
>> oneSiteSystemForce yes
>> }
>> }
>>
>> abf {
>> colvars COMDistance
>> fullSamples 1000
>> hidejacobian yes
>> }
>>
>> Other question, is better to separate the whole reaction coordinated in several windows, similar to the next work?
>>
>> dx.doi.org/10.1021/ci400188q <http://dx.doi.org/10.1021/ci400188q> J.Chem.Inf.Model.2013, 53, 2376−2389
>>
>> Thanks in advance.
>>
>> Gabriel
>>
>>
>> --
>> Dr. Gabriel E. Jara
>> Instituto de Química / UNICAMP
>> Rua Josué de Castro s/n
>> Cidade Universitária "Zeferino Vaz", Barão Geraldo
>> 13083-861 Campinas, São Paulo, Brasil
>> ------
>>
>
>
>
>
> --
> Dr. Gabriel E. Jara
> Instituto de Química / UNICAMP
> Rua Josué de Castro s/n
> Cidade Universitária "Zeferino Vaz", Barão Geraldo
> 13083-861 Campinas, São Paulo, Brasil
> ------
>
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