Re: NAMDenergy plugin_van der Waal interactions

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 21 2012 - 18:19:26 CST

Bruno,

it looks to me like Norman is confusing the
NAMDEnergy plugin with the NAMDPlot plugin.

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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