[gmx-users] different between g_hbond version
Dear all I have been using g_hbond of gromacs4.0.7 and 4.5.3 both gives me different results. is there any updates in the hbond tool E R Azhagiya singam -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
Re: [gmx-users] different between g_hbond version
Dear Erik which version of g_hbond is correct so that i ll use that for my analysis E R Azhagiya singam From: Erik Marklund er...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: babu gokul bb...@yahoo.co.in Sent: Mon, 14 February, 2011 4:20:32 PM Subject: Re: [gmx-users] different between g_hbond version babu gokul skrev 2011-02-14 11.28: Dear all I have been using g_hbond of gromacs4.0.7 and 4.5.3 both gives me different results. is there any updates in the hbond tool E R Azhagiya singam This has been reported but not fixed as far as I know. Embarresingly I'm probably the one who shoud fix it. I'll see what I can do. Erik -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] water hydration map analysis help
Dear all I would like to analysis the hydration site near the proteins the one done by the following paper Biophysical Journal Volume 79 December 2000 2966–2974 I would like to do the analysis the trajectory like this.is there any tool available in gromacs to do this kind of analysis could anyone help me in this regard. what tool will be useful to analysis this kind of results. Regards E R Azhagiya singam -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
[gmx-users] GridCount
Dear all I would like to analysis the hydration site near the proteins the one done by the following paper Biophysical Journal Volume 79 December 2000 2966–2974 I would like to do the analysis the trajectory like this. is this possible to do with GridCound tool if it is possible please explain the steps involved Regards E R Azhagiya singam -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
[gmx-users] Molecular dynamics hydration site
Dear all http://www.sciencedirect.com/science?_ob=MImg_imagekey=B94RW-4TYB1FX-K-1_cdi=56421_user=1245000_pii=S0006349500765337_coverDate=12/31/2000_sk=%23TOC%2356421%232000%23999209993%23703217%23FLA%23display%23Volume_79,_Issue_6,_Pages_2783-3354_(December_2000)%23tagged%23Volume%23first%3D79%23Issue%23first%3D6%23date%23(December_2000)%23view=c_gw=ywchp=dGLbVlb-zSkWbmd5=4e66a17da4627571bfd990beae45d486ie=/sdarticle.pdf I read the above linked paper about the to find a molecular density hydration map it says For each step of the MD trajectory, the protein was fitted to a consistent frame of reference. I did this by using trjconv i have fitted the protein in my trajectory Next, the same transformation was applied to the water molecule coordinates, taking the periodic boundaries into account. I did the same by using trjconv by using the trajectory i have obtained from the previous step The coordinates of the water oxygen atoms were then mapped onto the three-dimensional rectangular grid with a 0.5 Å grid step, producing an average three-dimensional number density distribution. The particular choice of the grid step is a compromise between the uncertainty in location of the density features and the statistical error in the local density value that arises due to a lower number of counts in each grid cell. At the chosen grid step every cell in the regions corresponding to bulk solvent would have at least 50 counts over the entire trajectory. The density map was smoothed by averaging the value of each cell with six of its nearest neighbors before further manipulations. I did the above step by using GridCount tool i got a grid.dat then i transformed the that to a vmd readable format density map. but when i visualize the file in vmd i got a lot of density over the corner but i was not able to visualize the it near the protein molecule as given in the above mentioned paper could anyone helpme in this regard how to do the same analysis in gromacs. Thanks in advance E R Azhagiya singam -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
[gmx-users] hydration maps
Dear all I would like to analysis the hydration site near the proteins the one done by the following paper Biophysical Journal Volume 79 December 2000 2966–2974 is there any tool available in gromacs to do this kind of analysis could anyone help me in this regard. what tool will be useful to analysis this kind of results. Regards E R Azhagiya singam -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
[gmx-users] About Zn paramter
Dear all I am including the parameter for the Zinc in the topology file all the bonded and nonbonded parameters have been included in the topology still it is not accepting the parameter the Zn atom move away from the coordination. Thanking you in advance E R Azhagiya singam -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
[gmx-users] reg. water mol. and its residence time
Dear friends I would like to get the water molecule residue no which is near a protein molecule active site and its residence time could anyone please help me in this regard Thanking you E R Azhagiya singam -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
[gmx-users] g_sorient
Dear all when i try to run g_sorient with g_sorient -f prod_full.xtc -s prod.tpr -o ANALYSIS/sorie nt/sori.xvg -no ANALYSIS/sorient/snor.xvg -ro ANALYSIS/sorient/sord.xvg I am getting a segmentation fault what would be the problem could anyone help in in this regard E R Azhagiya singam -- 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] intersting problem
dear all I want to calculate the how many water molecule are their with in 3.5 A of a particular atom. could anyone help me in this regard E R Azhagiya singam -- 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] about do_dssp
dear all I am analyzing a collagen dynamics i would like to analysis the collagen structure in and its parameter ? what is the difference between beta bridge and beta strand. thank you E R azhagiya singam -- 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] water mediated hydrogen bond
Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen mediated hydrogen bond. Thanking you E R Azhagiya singam -- 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] water mediated hydrogen bond
Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen mediated hydrogen bond. Thanking you E R Azhagiya singam -- 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] water Mediated Hydrogen Bond
Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen mediated hydrogen bond. Thanking you E R Azhagiya singam -- 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] about H-Bonds g_hbond
Hi all I am getting an error in g_hbond such as Program g_hbond_d, VERSION 4.0.7 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. Could anyone tell me how to solve this problem. thanks in advance E R Azhagiya singam Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php-- 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] Random Accelerator Molecular Dynamics
Hi all I would like to know whether Random Accelerator Molecular Dynamics is available in Gromacs as it is available in AMBER. E R Azhagiya singam -- 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] git installation error
I tried to install git version of Gromacs but when i make the file its shows the following error cc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\/usr/local/gromacs/share/top\ -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -I./include -MT nb_kernel400_ia32_sse.lo -MD -MP -MF .deps/nb_kernel400_ia32_sse.Tpo -c nb_kernel400_ia32_sse.c -o nb_kernel400_ia32_sse.o nb_kernel400_ia32_sse.c: In function `nb_kernel400_ia32_sse': nb_kernel400_ia32_sse.c:93: warning: implicit declaration of function `_mm_castsi128_ps' nb_kernel400_ia32_sse.c:93: error: invalid initializer nb_kernel400_ia32_sse.c:94: error: invalid initializer nb_kernel400_ia32_sse.c:95: error: invalid initializer make[5]: *** [nb_kernel400_ia32_sse.lo] Error 1 make[5]: Leaving directory `/git_gromacs/gromacs/src/gmxlib/nonbonded/nb_kernel_ia32_sse' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/git_gromacs/gromacs/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/git_gromacs/gromacs/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/git_gromacs/gromacs/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/git_gromacs/gromacs/src' make: *** [all-recursive] Error 1 could anyone help me in this regard E R Azhaigya singam Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/-- 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] about Git in Gromacs
Hi all I am new to git. when i tried to get the git version of gromacs by uisng the command git clone git://git.gromacs.org/gromacs.git in Cygwin i got an error saying Initialized empty Git repository in /home/admin/gromacs/.git/ fatal: Unable to look up git.gromacs.org (Unknown host) fetch-pack from 'git://git.gromacs.org/gromacs.git' failed could anyone help me in this regard I would be greatful to you. Thankyou E R Azhaigya singam The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- 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] About Zinc coordination
Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue. I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you E R Azhagiya singam Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/-- 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] About Zinc coordination
Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue. I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you E R Azhagiya singa Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/-- 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] (no subject)
Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue. I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you E R Azhagiya singam Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/-- 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
