AW: NAMDenergy plugin_van der Waal interactions

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Feb 22 2012 - 00:20:15 CST

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Axel Kohlmeyer
> Gesendet: Mittwoch, 22. Februar 2012 01:19
> An: Bruno Luís Pinto de Oliveira
> Cc: Norman Geist; Namd Mailing List
> Betreff: Re: namd-l: NAMDenergy plugin_van der Waal interactions
>
> Bruno,
>
> it looks to me like Norman is confusing the
> NAMDEnergy plugin with the NAMDPlot plugin.

True, sorry for that.

Norman Geist.

>
> from your description, it is very difficult to
> give advice (or else others would have) since
> you seem to be dealing with a "hard" problem.
>
> apart from the "mechanical" part of running
> namd through the namdenergy plugin on a
> subset of your system, there is the question
> of the validity of the results overall, since
> you are looking at organometallic compounds
> many of which are notoriously difficult to describe
> well with a classical potential in the first place
> and being quite challenging to QM/MM
> approaches as well.
>
> perhaps somebody that has - unlike me -
> worked on similar compounds can make
> some comments, but due to the many
> difficulties, people are not always very
> eager to share their experiences.
>
> axel.
>
> On Tue, Feb 21, 2012 at 7:05 PM, Bruno Luís Pinto de Oliveira
> <boliveira_at_itn.pt> wrote:
> > Dear Norman Geist,
> >
> > Thanks for your reply and advice.
> >
> > I was looking for something less time consuming because I'm finishing
> my thesis, but then I will follow your suggestion.
> >
> > I still have some difficulties to understand the utility of
> NAMDenergy...
> >
> > Best regards
> >
> > Bruno
> >
> .......................................................................
> .......................................................................
> ......
> > Bruno L. Oliveira
> > Radiopharmaceutical Sciences Group
> > Chemistry Department , ITN
> > http://www.itn.pt/sec/qui/qir/uk_qir_index.htm
> > http://www.boliveira.net
> >
> > ________________________________________
> > De: Norman Geist [norman.geist_at_uni-greifswald.de]
> > Enviado: terça-feira, 21 de Fevereiro de 2012 6:16
> > Para: Bruno Luís Pinto de Oliveira
> > Cc: Namd Mailing List
> > Assunto: AW: namd-l: NAMDenergy plugin_van der Waal interactions
> >
> > Hi,
> >
> > I guess what you need is to do some metadynamics. The namd energy
> plugin in
> > vmd only plots namd outfiles. You won't see the interaction clearly
> or not
> > in the global energy sums. With metadynamics you can collect such
> data to
> > analyze. NAMD has its own metadynamics implementation, but you can
> also use
> > it with plumed. You should inform about that.
> >
> > If what you see in your simulations is not the expected behavior,
> check your
> > parameters.
> >
> > Best wishes
> >
> > Norman Geist.
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> >> Auftrag von Bruno Luís Pinto de Oliveira
> >> Gesendet: Montag, 20. Februar 2012 14:01
> >> An: Chris Harrison
> >> Cc: namd-l_at_ks.uiuc.edu
> >> Betreff: RE: namd-l: NAMDenergy plugin_van der Waal interactions
> >>
> >> Hi everyone,
> >>
> >> I realized that my webpage was down. Perhaps this was the reason no
> one
> >> answered me (I was thinking the question didn't make a lot of
> sense).
> >>
> >> I will try again ;)
> >>
> >> I am simulating two organometallic compounds, which are very
> similar,
> >> complexed with the same protein (iNOS).
> >>
> >> The differences between the compounds is on the type of atoms that
> are
> >> coordenating the Metal(CO)3 core. The rest of the molecules is the
> >> same. Please find an image here for clarification:
> >>
> >> http://www.boliveira.net/NAMD4.html
> >>
> >> In one case the Rhenium(CO)3 is well accomodated inside the active
> >> pocket (better inhibitor), while in the ohter case after 3ns the
> >> Rhenium(CO)3 is oriented toward the peripheral pocket situated  at
> the
> >> surface of the enzyme (worst inhibitor).
> >>
> >> I would like to know if I can use the NAMDenergy plugin to analyse
> the
> >> vdwaals interactions between the Rhenium(CO)3 part and the residues
> of
> >> the active pocket to identify which residues contribute for the
> >> repulsion or stability of the Re(CO)3? (considering that less
> positive
> >> vdwaals energy = more stable = less repulsion; more positive vdwaals
> =
> >> less stable = more repulsion).
> >>
> >> Can I also use the electrostatic energies to identify which residues
> >> contribute for stabilization of the Rhenium(CO)3 part inside the
> active
> >> pocket (in the case of the better inhibitor)?
> >>
> >> If not can someone suggest me please another approach to trying to
> get
> >> an understanding why in one case the Re(CO)3 core is accomodated
> inside
> >> the active pocket and in the other case  is repulsed.
> >>
> >> Thank you in advance
> >>
> >> Regards
> >>
> >> Bruno
> >>
> .......................................................................
> >>
> .......................................................................
> >> ......
> >> Bruno L. Oliveira
> >> Radiopharmaceutical Sciences Group
> >> Chemistry Department , ITN
> >> http://www.itn.pt/sec/qui/qir/uk_qir_index.htm
> >> http://www.boliveira.net
> >>
> >> ________________________________________
> >> De: Chris Harrison [charris5_at_gmail.com]
> >> Enviado: quarta-feira, 15 de Fevereiro de 2012 21:27
> >> Para: Bruno Luís Pinto de Oliveira
> >> Cc: namd-l_at_ks.uiuc.edu
> >> Assunto: Re: namd-l: NAMDenergy plugin_van der Waal interactions
> >>
> >> Dear Bruno,
> >>
> >> 1) Your site, www.boliveira.com, appears to be dead, so I couldn't
> see
> >> the image.
> >>
> >> 2) Yes you can measure the VDW with NAMDEnergy, however you don't
> >> mention electrostatics in your message.  You may want to also
> >> investigate the electrostatic interactions which predominate over
> VDW
> >> at longer ranges.
> >>
> >> Best,
> >> Chris
> >>
> >>
> >>
> >> On Thu, Feb 2, 2012 at 11:06 AM, Bruno Luís Pinto de Oliveira
> >> <boliveira_at_itn.pt> wrote:
> >> > Hi everyone,
> >> >
> >> > I am simulating two organometallic coumpounds, which are very
> >> similar, complexed with the same protein (iNOS).
> >> >
> >> > The differences between the compounds is on the type of atoms that
> >> are coordenating the Rhenium(CO)3 core. The rest of the molecules is
> >> the same. Please find an image here for clarification:
> >> >
> >> > http://www.boliveira.com/NAMD4.html
> >> >
> >> > In one case the Rhenium(CO)3 is well accomodated inside the active
> >> pocket (better inhibitor), while in the ohter case after 3ns the
> >> Rhenium(CO)3 is oriented toward the peripheral pocket situated  at
> the
> >> surface of the active site (worst inhibitor).
> >> >
> >> > I would like to know if I can use the NAMDenergy plugin to analyse
> >> the vdwaal interactions between the Rhenium(CO)3 part and the
> residues
> >> of the active pocket to indentify which residues contribute for the
> >> repulsion or stability of the Re(CO)3? (considering that less
> positive
> >> vdwaal energy = more stable = less repulsion and more positive
> vdwaal =
> >> less stable = more repulsion).
> >> >
> >> > If not can someone suggest me another aproach to trying to get an
> >> understanding of the contributions to protein-ligand stabilities.
> >> >
> >> > Thank you
> >> >
> >> > Regards
> >> >
> >> >
> >>
> .......................................................................
> >>
> .......................................................................
> >> ......
> >> > Bruno L. Oliveira
> >> > Radiopharmaceutical Sciences Group
> >> > Chemistry Department , ITN
> >> > http://www.itn.pt/sec/qui/qir/uk_qir_index.htm
> >> > http://www.boliveira.com
> >> >
> >> >
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Chris Harrison, Ph.D.
> >> Theoretical and Computational Biophysics Group
> >> NIH Resource for Macromolecular Modeling and Bioinformatics
> >> Beckman Institute for Advanced Science and Technology
> >> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> >>
> >> char_at_ks.uiuc.edu                            Voice: 773-570-6078
> >> http://www.ks.uiuc.edu/~char                Fax: 217-244-6078
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

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