[gmx-users] Re: gmx-users Digest, Vol 89, Issue 83

[גדעון לפידות]

Hello GMX users,

I have a couple of questions regrading energy run and g_lie:
1. I am interested in calculating the estimated binding energy between pip2
and a protein using the lie method.
2. I have run the protein ligand  complex for 40 ns with counter-ions,
npt ensemble and PME
3. In order to calculate the ligand -sol Eqq and Elj I have run the ligand
for 10 ns , also adding counter ions.
4. The resulting energies from the solvated ligand were around -3000 KJ
of electrostatic energy and about +200 KJ of lj energy.

So what I am asking is first, is it fair to assume that the positive LJ
value of the ligand solvent energy is due to the high electrostatics energy
between ligand and sol?
And secondly, since the sol-lig elec. energy is much higher than lig-prot
elec. energy doing simple lie calculation provides a positive binding
energy, which obviously contradicts the biology. So is the whole calculation
not valid or can I do some tweaking with lie formula (for instance change
the alpha and beta parameters) to try and reproduce experimental data.

Thanks,

Gideon

and second


2011/9/14 <gmx-users-request at gromacs.org>

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> Today's Topics:
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>   1. Re: installation of FFTW (Mark Abraham)
>   2. Potential energy problem (madhumita das)
>   3. Re: Potential energy problem (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 14 Sep 2011 15:28:30 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] installation of FFTW
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E703B7E.7020409 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 14/09/2011 3:24 PM, ITHAYARAJA wrote:
> >
> > Hi
> >
> > I am working with RHEL 6 beta, I unable to install the FFTW package
> > while installation I found the following error,
>
> There is no error reported in what you have shown.
>
> >
> >
> > make[3]: Leaving directory `/home/Ithayaraja/Desktop/
> > fftw-3.3.1-beta1/tools'
> > make[2]: Leaving directory
> > `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools'
> > Making all in m4
> > make[2]: Entering directory
> `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'
> > make[2]: Nothing to be done for `all'.
> > make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'
> > make[1]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1'
> >
> >
> > can you help me to find out where i did wrong?
>
> Not without knowing your configure line, knowing that you have followed
> the instructions on the GROMACS webpage, seeing what the actual error
> message was, and knowing why you're trying to use a beta of a version of
> FFTW that is a few years out of date. :)
>
> Mark
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 14 Sep 2011 12:59:42 +0530
> From: madhumita das <madhumita.bioinfo at gmail.com>
> Subject: [gmx-users] Potential energy problem
> To: gmx-users at gromacs.org
> Message-ID:
>        <CAFa+f=G5hjY62-pPD48BS1y0tvtDOMVLC1EJYeS=Y_Yz808MdQ at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Gromacs users,
>
> I am doing the protein lipid system packing step and thus shrinking and
> minimizing the system alternately but after first minimization rest of all
> minimization steps show E pot=nan and no minimization step occurs in the
> em.log file. How to get rid of this problem? Please help.
>
>
> Yours faithfully,
>
> Madhumita Das.
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> ------------------------------
>
> Message: 3
> Date: Wed, 14 Sep 2011 17:48:52 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Potential energy problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E705C64.1020105 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 14/09/2011 5:29 PM, madhumita das wrote:
> > Hi Gromacs users,
> >
> > I am doing the protein lipid system packing step and thus shrinking
> > and minimizing the system alternately but after first minimization
> > rest of all minimization steps show E pot=nan and no minimization step
> > occurs in the em.log file. How to get rid of this problem? Please help.
>
> It is likely that your system is
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> Mark
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 89, Issue 83
> *****************************************
>


-- 

Gideon Lapidoth,

MS.c candidate

Hemi Gutman Biophysics Lab

Department of Biochemistry & Molecular Biology

George S. Wise Faculty of Life Sciences

Tel Aviv University

Israel 69978

<http://ashtoret.tau.ac.il/>

Tel: (972-3) 640-9824
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