Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs

From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Dec 12 2013 - 19:25:58 CST

I may be missing something crucial in terms of what SMD does, but wouldn't
running it without that harmonic restraint be meaningless? What I mean is,
don't you want to steer the ligand relative to the protein? So either you
should perform this steering on the distance between the protein and
ligand, or, you just do the ligand but hold the protein fixed (with say a
harmonic restraint on the Ca as you say).

I've never done SMD, and don't know much about how it is supposed to work,
but if all you do is yank on the ligand, the only information I can see you
getting from that is maybe something relating to the energy barrier for
ligand dissociation, and by that I mean the kinetic one, not the
thermodynamic one.

Are you sure in the Gromacs case it wasn't the distance between the ligand
and protein that was being steered? Or maybe the restraint is implicitly
assumed and that's why they don't mention it?

On Thu, Dec 12, 2013 at 8:02 PM, dbaogen <dbaogen_at_gmail.com> wrote:

> Hi,
>
> Thanks for your suggestion. Using SMD in NAMD software, if we impose
> harmonic restriction on the center of alpha carbons of protein, the ligand
> can be pulled out. But I am not sure whether this will introduce artificial
> effect on the simulated system. Would you like to give me some suggestions
> about the simulation. Thanks.
>
> Best
> Duan Baogen
>
>
> *From:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Date:* 2013-12-10 22:18
> *To:* 'dbaogen' <dbaogen_at_gmail.com>
> *CC:* Namd Mailing List <namd-l_at_ks.uiuc.edu>
> *Subject:* AW: namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
>
> Hi,
>
> I donít think that this is a problem of the implementatio of the pulling.
> Itís more likely a stronger interaction between your protein and the ligand
> than in the publication you found. Maybe you could give the proteins center
> of mass a counter force.
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *dbaogen
> *Gesendet:* Dienstag, 10. Dezember 2013 13:02
> *An:* namd-l
> *Betreff:* namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
>
>
>
> Dear all,
>
>
>
> Recently, I have a problem in using SMD to pull a ligand out
> from the protein active site. In the course of pulling, the protein is
> moving along with ligand. So the results are not consistent with our
> expectation. If we impose the harmonic restraint on protein, the ligand can
> be pulled out. But the artificial effect would be introduced if we did it
> like that. Would anyone like to give me some suggestions about the SMD
> simulation in NAMD?
>
>
>
> In addition, it is found that the pull code in Gromacs can also
> do the SMD simulation. From the published results using pull code in
> Gromacs, the protein itself was not restricted while pulling a ligand out
> from the protien's active site. Would you like to explain the difference
> between SMD in NAMD and pull code in Gromacs? Thanks in advance!
>
>
>
> Best
>
>
>
> Duan Baogen
>
>
> ------------------------------
> <http://www.avast.com/>
>
> Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus<http://www.avast.com/>Schutz ist aktiv.
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:24:05 CST