Re: [gmx-users] gromacs result
Maik Goette wrote: Right, but I can just warn anyone. Trying to use TI on a docked structure is insanity... The docked structure is an approximation in its best case (more likely its simply crap). Applying a free energy calculation towards such a structure will give you everything...but sure not the the correct free energy of bindingexcept you are very luckyIF you are that lucky, play lottery instead and enjoy life ;) In fact it's (citating Mark) another expensive random number generator... I think you're exaggerating a bit. Docking works quite well if you do it correctly, that is many (>=100) tries. See my website below for some useful publications on docking... -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs result
Right, but I can just warn anyone. Trying to use TI on a docked structure is insanity... The docked structure is an approximation in its best case (more likely its simply crap). Applying a free energy calculation towards such a structure will give you everything...but sure not the the correct free energy of bindingexcept you are very luckyIF you are that lucky, play lottery instead and enjoy life ;) In fact it's (citating Mark) another expensive random number generator... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: mahbubeh zarrabi wrote: Dear all I have 3 complexes of docking.(one receptor with 3 different ligands).I studied MD of 3 complexes in 15 ns by gromacs.how can i compare binding energy and affinity of 3 ligands with receptor.(how can i analysis gromacs result) Shouldn't you have asked this question before designing your simulations? :-) You can't measure binding affinity without taking a difference between "before" and "after", which you don't seem to have. You probably need to look at literature on thermodynamic integration, or some such. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs result
mahbubeh zarrabi wrote: Dear all I have 3 complexes of docking.(one receptor with 3 different ligands).I studied MD of 3 complexes in 15 ns by gromacs.how can i compare binding energy and affinity of 3 ligands with receptor.(how can i analysis gromacs result) Shouldn't you have asked this question before designing your simulations? :-) You can't measure binding affinity without taking a difference between "before" and "after", which you don't seem to have. You probably need to look at literature on thermodynamic integration, or some such. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs result
Dear all I have 3 complexes of docking.(one receptor with 3 different ligands).I studied MD of 3 complexes in 15 ns by gromacs.how can i compare binding energy and affinity of 3 ligands with receptor.(how can i analysis gromacs result) thanks Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
