<div dir="rtl"><div dir="ltr">Hello GMX users,</div><div dir="ltr"><br></div><div dir="ltr">I have a couple of questions regrading energy run and g_lie:</div><div dir="ltr">1. I am interested in calculating the estimated binding energy between pip2 and a protein using the lie method.</div>
<div dir="ltr">2. I have run the protein ligand complex for 40 ns with counter-ions, npt ensemble and PME</div><div dir="ltr">3. In order to calculate the ligand -sol Eqq and Elj I have run the ligand for 10 ns , also adding counter ions.</div>
<div dir="ltr">4. The resulting energies from the solvated ligand were around -3000 KJ of electrostatic energy and about +200 KJ of lj energy.</div><div dir="ltr"><br></div><div dir="ltr">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?</div>
<div dir="ltr">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.</div>
<div dir="ltr"><br></div><div dir="ltr">Thanks,</div><div dir="ltr"><br></div><div dir="ltr">Gideon </div><div dir="ltr"><br></div><div dir="ltr">and second </div><div dir="ltr"><br><br><div class="gmail_quote">
2011/9/14 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br>
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1. Re: installation of FFTW (Mark Abraham)<br>
2. Potential energy problem (madhumita das)<br>
3. Re: Potential energy problem (Mark Abraham)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 14 Sep 2011 15:28:30 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] installation of FFTW<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E703B7E.7020409@anu.edu.au" target="_blank">4E703B7E.7020409@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 14/09/2011 3:24 PM, ITHAYARAJA wrote:<br>
><br>
> Hi<br>
><br>
> I am working with RHEL 6 beta, I unable to install the FFTW package<br>
> while installation I found the following error,<br>
<br>
There is no error reported in what you have shown.<br>
<br>
><br>
><br>
> make[3]: Leaving directory `/home/Ithayaraja/Desktop/<br>
> fftw-3.3.1-beta1/tools'<br>
> make[2]: Leaving directory<br>
> `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools'<br>
> Making all in m4<br>
> make[2]: Entering directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'<br>
> make[2]: Nothing to be done for `all'.<br>
> make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'<br>
> make[1]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1'<br>
><br>
><br>
> can you help me to find out where i did wrong?<br>
<br>
Not without knowing your configure line, knowing that you have followed<br>
the instructions on the GROMACS webpage, seeing what the actual error<br>
message was, and knowing why you're trying to use a beta of a version of<br>
FFTW that is a few years out of date. :)<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 14 Sep 2011 12:59:42 +0530<br>
From: madhumita das <<a href="mailto:madhumita.bioinfo@gmail.com" target="_blank">madhumita.bioinfo@gmail.com</a>><br>
Subject: [gmx-users] Potential energy problem<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<CAFa+f=G5hjY62-pPD48BS1y0tvtDOMVLC1EJYeS=<a href="mailto:Y_Yz808MdQ@mail.gmail.com" target="_blank">Y_Yz808MdQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Gromacs users,<br>
<br>
I am doing the protein lipid system packing step and thus shrinking and<br>
minimizing the system alternately but after first minimization rest of all<br>
minimization steps show E pot=nan and no minimization step occurs in the<br>
em.log file. How to get rid of this problem? Please help.<br>
<br>
<br>
Yours faithfully,<br>
<br>
Madhumita Das.<br>
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<br>
Message: 3<br>
Date: Wed, 14 Sep 2011 17:48:52 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Potential energy problem<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E705C64.1020105@anu.edu.au" target="_blank">4E705C64.1020105@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 14/09/2011 5:29 PM, madhumita das wrote:<br>
> Hi Gromacs users,<br>
><br>
> I am doing the protein lipid system packing step and thus shrinking<br>
> and minimizing the system alternately but after first minimization<br>
> rest of all minimization steps show E pot=nan and no minimization step<br>
> occurs in the em.log file. How to get rid of this problem? Please help.<br>
<br>
It is likely that your system is<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up" target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br>
<br>
Mark<br>
<br>
<br>
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End of gmx-users Digest, Vol 89, Issue 83<br>
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</font></blockquote></div></div><br clear="all"><div><br></div>-- <br><div dir="rtl"><div dir="ltr"><p>Gideon Lapidoth,</p><p>MS.c candidate</p><p>Hemi Gutman Biophysics Lab<br></p><p>Department of Biochemistry & Molecular Biology </p>
<p>George S. Wise Faculty of Life Sciences </p><p>Tel Aviv University</p><p>Israel 69978 </p><p><a href="http://ashtoret.tau.ac.il/" target="_blank"></a> </p><p>Tel: (972-3) 640-9824 <br></p><p> <br></p></div></div>
<br>
</div>