בתאריך 15 בספטמבר 2011 12:58, מאת גדעון לפידות <glapid...@gmail.com>:
> 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-requ...@gromacs.org> > > Send gmx-users mailing list submissions to >> gmx-users@gromacs.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> or, via email, send a message with subject or body 'help' to >> gmx-users-requ...@gromacs.org >> >> You can reach the person managing the list at >> gmx-users-ow...@gromacs.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gmx-users digest..." >> >> >> Today's Topics: >> >> 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.abra...@anu.edu.au> >> Subject: Re: [gmx-users] installation of FFTW >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <4e703b7e.7020...@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.bioi...@gmail.com> >> Subject: [gmx-users] Potential energy problem >> To: gmx-users@gromacs.org >> Message-ID: >> <CAFa+f=G5hjY62-pPD48BS1y0tvtDOMVLC1EJYeS= >> y_yz808...@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. >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110914/470889d8/attachment-0001.html >> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 14 Sep 2011 17:48:52 +1000 >> From: Mark Abraham <mark.abra...@anu.edu.au> >> Subject: Re: [gmx-users] Potential energy problem >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <4e705c64.1020...@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 >> >> >> ------------------------------ >> >> -- >> gmx-users mailing list >> gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >> 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 > > > > -- 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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