[gmx-users] cross-correlations as a function of interatomic distance
Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] free energy calculations for two ligands
Dear All, I have a trimeric protein system which binds to two different ligands. The ligands are oligosaccharides. The difference between the two is first ligand has beta 1-4 linkage and the second ligand has beta 1-3 linkage between Galactose (Gal) and N-Acetyl Glucosamine (GlcNAc). Since the linkage changes I have changes in atoms, bonds, pairs, angles and dihedrals. In the pair and dihedrals, some of the pairs are present in the first ligand and not in the second ligand. How do I make the topology for the change from ligand A to ligand B in the free energy simulations? The same is the case with dihedrals. Angles, bonds and atoms have no problem. Can someone please help me in this regard? Thanks for your time. Regards Sai -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LIE energy values for dimers
Thanks a lot professor Spoel! > On 2010-03-13 20.13, jorge_quint...@ciencias.uis.edu.co wrote: >> Dear all >> >> I used LIE method in order to obtain information related with free >> energy >> bind between two proteins. Previously, I obtained several dimeric >> configuration using zdock package, and geometry optimization for each >> model. For the first ten complex, I used LIE. These are my results: >> >> complex1 -2267.44 >> complex2 -2191.92 >> complex3 -2136.47 >> complex4 -2430.13 >> complex5 -2227.88 >> complex6 -2476.61 >> complex7 -2327.87 >> complex8 -2219.41 >> complex9 -2299.76 >> complex10 -2324.9 >> >> Are these value correct?. I'll appreciate your support! >> > Impossible to say. I don't know whether there is any accepted protocol > for this purpose, but LIE is probably too crude. There a couple of > servers out there that will give you a value. Search for protein-protein > interaction prediction or something like that. > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LIE energy values for dimers
On 2010-03-13 20.13, jorge_quint...@ciencias.uis.edu.co wrote: Dear all I used LIE method in order to obtain information related with free energy bind between two proteins. Previously, I obtained several dimeric configuration using zdock package, and geometry optimization for each model. For the first ten complex, I used LIE. These are my results: complex1 -2267.44 complex2 -2191.92 complex3 -2136.47 complex4 -2430.13 complex5 -2227.88 complex6 -2476.61 complex7 -2327.87 complex8 -2219.41 complex9 -2299.76 complex10 -2324.9 Are these value correct?. I'll appreciate your support! Impossible to say. I don't know whether there is any accepted protocol for this purpose, but LIE is probably too crude. There a couple of servers out there that will give you a value. Search for protein-protein interaction prediction or something like that. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LIE energy values for dimers
Dear all I used LIE method in order to obtain information related with free energy bind between two proteins. Previously, I obtained several dimeric configuration using zdock package, and geometry optimization for each model. For the first ten complex, I used LIE. These are my results: complex1 -2267.44 complex2 -2191.92 complex3 -2136.47 complex4 -2430.13 complex5 -2227.88 complex6 -2476.61 complex7 -2327.87 complex8 -2219.41 complex9 -2299.76 complex10 -2324.9 Are these value correct?. I'll appreciate your support! -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_hbond
On 2010-03-13 09.40, shahab shariati wrote: I used g_hbond for analysis of hydrogen bonds. g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm -don -dan -life -nhbdist -a 30 -r 0.35 Following text was turned up: ACF 288/288 Normalization for c(t) = 0.0204067 for gh(t) = 8.10294e-06 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) > 0.001 Tail value (average C(t) over second half of acf): 0.685894 +/- 0.00448515 You should do a *much* longer simulation. Since the forward rate for breaking is 65 ps you should do at least 10-20 ns. Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0199698 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 0.015 65.068 14.879 0.0199698 Backward 0.009 108.405 16.144 One-way 0.020 48.818 14.166 Integral 0.007 143.963 16.847 Relaxation 0.085 11.787 10.644 HB lifetime = 10.98 ps Note that the lifetime obtained in this manner is close to useless Use the -ac option instead and check the Forward lifetime *Is my manner wrong? * * * *What job Should be done?* -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_hbond
I used g_hbond for analysis of hydrogen bonds. g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm -don -dan -life -nhbdist -a 30 -r 0.35 Following text was turned up: ACF 288/288 Normalization for c(t) = 0.0204067 for gh(t) = 8.10294e-06 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) > 0.001 Tail value (average C(t) over second half of acf): 0.685894 +/- 0.00448515 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0199698 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 0.015 65.068 14.879 0.0199698 Backward0.009108.405 16.144 One-way 0.020 48.818 14.166 Integral0.007143.963 16.847 Relaxation 0.085 11.787 10.644 HB lifetime = 10.98 ps Note that the lifetime obtained in this manner is close to useless Use the -ac option instead and check the Forward lifetime *Is my manner wrong? * * * *What job Should be done?* -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
