Re: [gmx-users] angle between helices
On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. cheers, marc ___ 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] angle between helices
Marc F. Lensink wrote: On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. otherwise g_bundle might do it cheers, marc ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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] angle between helices
On Mon, Oct 29, 2007 at 09:54:08AM +0100, David van der Spoel wrote: Marc F. Lensink wrote: On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. otherwise g_bundle might do it yes, i should perhaps mention that my program calculates the helix axes, using some rotational fit. but for TM helices, that stay helix anyway, this is not such a relevant feature. cheers, marc ___ 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] angle between helices
HI David there are options like g_helix, g_angle and as you said g_bundle, but none of them gives the angle between helix pairs. anupam Marc F. Lensink wrote: On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. otherwise g_bundle might do it cheers, marc ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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] angle between helices
g_bundle does give the angle between helix pairs...? Not directly, admittedly, but it gives you the tilt from the main axes, which you can use with some basic math to work out the angle between helices. - Original Message From: Anupam Nath Jha [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, October 29, 2007 10:37:13 AM Subject: Re: [gmx-users] angle between helices HI David there are options like g_helix, g_angle and as you said g_bundle, but none of them gives the angle between helix pairs. anupam Marc F. Lensink wrote: On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. otherwise g_bundle might do it cheers, marc ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] x2top problem
Dear all, I have a problem in the generation of the topology file of a ligand using x2top program. I think that it's a problem with the detection of the connectivity by the program.I am using the version 3.3.2 of Gromacs. As an example i have take only a fragment of my molecule, that it's a benzamidine group. ATOM 1 C ABK 0 -1.230 -1.842 0.078 C ATOM 2 C ABK 0 -0.039 0.308 0.150 C ATOM 3 C ABK 0 0.010 -2.531 0.093 C ATOM 4 C ABK 0 1.225 -1.801 0.134 C ATOM 5 C ABK 0 1.200 -0.384 0.164 C ATOM 6 C ABK 0 -0.046 2.022 0.175 C ATOM 7 C ABK 0 -1.254 -0.424 0.102 C ATOM 8 H ABK 0 -2.193 -2.420 0.045 H ATOM 9 H ABK 0 0.029 -3.654 0.071 H ATOM 10 H ABK 0 -1.494 2.171 1.516 H ATOM 11 H ABK 0 -0.807 3.690 0.913 H ATOM 12 H ABK 0 1.997 2.551 -0.694 H ATOM 13 H ABK 0 0.660 3.385 -1.519 H ATOM 14 H ABK 0 2.163 0.193 0.197 H ATOM 15 H ABK 0 2.208 -2.346 0.142 H ATOM 16 H ABK 0 -2.237 0.119 0.084 H ATOM 17 N ABK 0 -0.826 2.661 0.908 N ATOM 18 N ABK 0 0.999 2.793 -0.751 N CONECT712 16 CONECT1738 CONECT2756 CONECT3149 CONECT435 15 CONECT524 14 CONECT62 17 18 CONECT 176 10 11 CONECT 186 12 13 when i run x2top program i obtained: WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /software2/gromacs-3.3.2/exe/share/gromacs/top/aminoacids.dat Opening library file /software2/gromacs-3.3.2 /exe/share/gromacs/top/atommass.dat Opening library file /software2/gromacs-3.3.2 /exe/share/gromacs/top/vdwradii.dat Opening library file /software2/gromacs-3.3.2/exe/share/gromacs/top/dgsolv.dat #Entries in atommass.dat: 83 vdwradii.dat: 27 dgsolv.dat: 7 Looking whether force field files exist Opening library file /software2/gromacs-3.3.2 /exe/share/gromacs/top/ffoplsaa.rtp Opening library file ffoplsaa.n2t WARNING: all CONECT records are ignored Opening library file ffoplsaa.n2t There are 21 name to type translations Generating bonds from distances... atom 18 Can not find forcefield for atom C-2 with 2 bonds Can not find forcefield for atom C-6 with 1 bonds Can not find forcefield for atom N-17 with 2 bonds Can not find forcefield for atom N-18 with 3 bonds --- Program x2top, VERSION 3.3.2 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 14 out of 18 atoms I know that i can add these atoms to the ffoplsaa.n2t file. But what i don't understand is that the program says that C6 atom is attached by 1 bond, whereas in fact it's attached to 3 atoms. C2 has 3 bonds (not 2) and N17 has 3 bonds (not 2). I tried to include the atoms in the ffoplsaa.n2t but i must did it in the wong connectivity. Thanks in avance for your help and best regards, Patricia ___ 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] Running Gromacs on the Grid Workshop 14.-15.11.
Running Gromacs on the Grid 14.-15.11., at CSC, Espoo, Finland. CSC will organise a workshop to show how to run Gromacs jobs in MGrid and other NorduGrid clusters. The hands-on examples are chosen to illustrate how to use simultaneous serial simulations effectively and that methodology is, of course, usable also outside ARC-based grids. Gromacs developers Erik Lindahl and Berk Hess and Grid specialists from CSC are available to answer your questions and tutor the hands-on exercises. The Workshop is sponsored by NDGF (Nordic Data Grid Facility) and participants from Scandinavia and the Baltic region have precedence. The registration ends by Monday 5th November at 12:00 so be quick! Registration and more information: http://www.csc.fi/english/csc/courses/archive/Grid-gmx07 Cheers, Atte -- Atte Sillanpää, Application specialist, Chemistry Support CSC - IT Center of Science, Po Box 405, 02101 Espoo, FINLAND TEL +358 9 457 2250, www.csc.fi, email [EMAIL PROTECTED]___ 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] what do negative eigenvalues imply?
Hello, I was wondering if anybody can explain why eigenvalues can be negative? I have found a suggestion on the internet that this is because the positive eigenvalues have accounted for more than 100% of the motion. Does this sound accurate? This system is the alanine dipeptide. I do not find such negative values when running g_covar on full proteins. The contents of eigenval.xvg are listed below. # This file was created Mon Oct 29 16:31:46 2007 # by the following command: # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar -s ../adp.tpr -n ../adp.ndx -f ../adp_0-1.56us.xtc -ascii covar.dat -mwa # # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar is part of G R O M A C S: # # Great Red Owns Many ACres of Sand # @title Eigenvalues of the covariance matrix @xaxis label Eigenvector index @yaxis label (u nm\S2\N) @TYPE xy 1 0.211327 2 0.0736961 3 0.0522046 4 0.04409 5 0.0104057 6 0.00577603 7 0.00198832 8 0.00163465 9 0.00128302 10 0.000735383 11 0.000649576 12 0.000434795 13 0.000376401 14 0.000337852 15 0.000191994 16 0.000131498 17 8.87514e-05 18 7.31975e-05 19 5.31939e-05 20 4.45637e-05 21 -5.03112e-06 22 -1.26812e-05 23 -2.48763e-05 24 -5.90268e-05 25 -0.000114215 26 -0.000227912 27 -0.000355243 28 -0.000513052 29 -0.000631471 30 -0.00178302 ___ 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] what do negative eigenvalues imply?
Chris Neale wrote: Hello, I was wondering if anybody can explain why eigenvalues can be negative? I have found a suggestion on the internet that this is because the positive eigenvalues have accounted for more than 100% of the motion. Does this sound accurate? No You normally have six negative eigevalues due to the fact that overall translation and rotation are removed. You have in addition 4 that are very small, maybe you can investigate how many degrees of freedom you have (it says in the md.log file). This should be equal to the umber of non-negative ev. This system is the alanine dipeptide. I do not find such negative values when running g_covar on full proteins. The contents of eigenval.xvg are listed below. # This file was created Mon Oct 29 16:31:46 2007 # by the following command: # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar -s ../adp.tpr -n ../adp.ndx -f ../adp_0-1.56us.xtc -ascii covar.dat -mwa # # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar is part of G R O M A C S: # # Great Red Owns Many ACres of Sand # @title Eigenvalues of the covariance matrix @xaxis label Eigenvector index @yaxis label (u nm\S2\N) @TYPE xy 1 0.211327 2 0.0736961 3 0.0522046 4 0.04409 5 0.0104057 6 0.00577603 7 0.00198832 8 0.00163465 9 0.00128302 10 0.000735383 11 0.000649576 12 0.000434795 13 0.000376401 14 0.000337852 15 0.000191994 16 0.000131498 17 8.87514e-05 18 7.31975e-05 19 5.31939e-05 20 4.45637e-05 21 -5.03112e-06 22 -1.26812e-05 23 -2.48763e-05 24 -5.90268e-05 25 -0.000114215 26 -0.000227912 27 -0.000355243 28 -0.000513052 29 -0.000631471 30 -0.00178302 ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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
[gmx-users] what do negative eigenvalues imply?
/ Hello, // // I was wondering if anybody can explain why eigenvalues can be negative? // I have found a suggestion on the internet that this is because the // positive eigenvalues have accounted for more than 100% of the motion. // Does this sound accurate? / No You normally have six negative eigevalues due to the fact that overall translation and rotation are removed. You have in addition 4 that are very small, maybe you can investigate how many degrees of freedom you have (it says in the md.log file). This should be equal to the umber of non-negative ev. Thanks for the explanation David. I have selected only the heavy atoms in the alanine dipeptide for the previously posted analysis. Therefore I made a new temperature coupling group composed only of these atoms and ran grompp in order to get the desired value output: Number of degrees of freedom in T-Coupling group Protein_NoH is 23.98 So 24-6 is 18 and I am positive up to 20. I suppose it is ok that there are more (small) positive values than 18. If I re-do the analysis instead using all 22 atoms (include the H's) then grompp indicates: Number of degrees of freedom in T-Coupling group Protein is 53.96 And I am positive up to ev #41 (g_covar eigenval.xvg follows) so 54-6 is 48, but I only have 41 positive. Nevertheless, the ev 42-48 are very small positive. # This file was created Mon Oct 29 18:45:06 2007 # by the following command: # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar -s ../adp.tpr -n ../adp.ndx -f ../adp_0-1.56us.xtc -ascii covar.dat -mwa # # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar is part of G R O M A C S: # # Gnomes, ROck Monsters And Chili Sauce # @title Eigenvalues of the covariance matrix @xaxis label Eigenvector index @yaxis label (u nm\S2\N) @TYPE xy 1 0.23291 2 0.0810199 3 0.0579589 4 0.0430226 5 0.0156911 6 0.015543 7 0.0154095 8 0.0153563 9 0.0153322 10 0.0151271 11 0.0122578 12 0.00725067 13 0.00261468 14 0.00179256 15 0.00165951 16 0.00103279 17 0.000815341 18 0.000572039 19 0.000508098 20 0.000365606 21 0.000359221 22 0.000352105 23 0.00035001 24 0.000344526 25 0.000259272 26 0.000258307 27 0.000251824 28 0.000201794 29 0.000134211 30 0.0001308 31 0.00010905 32 0.000107029 33 8.21594e-05 34 7.64162e-05 35 6.1539e-05 36 4.31456e-05 37 3.68485e-05 38 2.35955e-05 39 2.11371e-05 40 1.34103e-05 41 6.81332e-06 42 -1.17905e-06 43 -4.04147e-06 44 -9.72161e-06 45 -1.3889e-05 46 -3.51393e-05 47 -4.49705e-05 48 -6.51993e-05 49 -6.75307e-05 50 -7.47012e-05 51 -8.77501e-05 52 -0.00010138 53 -0.000103669 54 -0.000105253 55 -0.000106886 56 -0.000110613 57 -0.000111074 58 -0.000134431 59 -0.000166161 60 -0.000180943 61 -0.000204832 62 -0.000298183 63 -0.000444828 64 -0.00052514 65 -0.000592853 66 -0.00213633 Thanks, Chris. / // This system is the alanine dipeptide. I do not find such negative values // when running g_covar on full proteins. // // The contents of eigenval.xvg are listed below. // // # This file was created Mon Oct 29 16:31:46 2007 // # by the following command: // # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar // -s ../adp.tpr -n ../adp.ndx -f ../adp_0-1.56us.xtc -ascii covar.dat -mwa // # // is part of G R O M A C S: // # // # Great Red Owns Many ACres of Sand // # // @title Eigenvalues of the covariance matrix // @xaxis label Eigenvector index // @yaxis label (u nm\S2\N) // @TYPE xy // 1 0.211327 // 2 0.0736961 // 3 0.0522046 // 4 0.04409 // 5 0.0104057 // 6 0.00577603 // 7 0.00198832 // 8 0.00163465 // 9 0.00128302 //10 0.000735383 //11 0.000649576 //12 0.000434795 //13 0.000376401 //14 0.000337852 //15 0.000191994 //17 8.87514e-05 //18 7.31975e-05 //19 5.31939e-05 //20 4.45637e-05 //21 -5.03112e-06 //22 -1.26812e-05 //23 -2.48763e-05 //24 -5.90268e-05 //25 -0.000114215 //26 -0.000227912 //27 -0.000355243 //28 -0.000513052 //29 -0.000631471 //30 -0.00178302/ ___ 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
