[gmx-users] restraints or constraints over two molecules
hi, i want to ask if there is a possibility to make distance restraints or contraints over two molecules? till now i have two .itp files (one for each molecule) and i include them with 'inculde ...itp . after that i have [ system ] and [ molecules ] (with my two molecules) and then [ distance_restraints ] respectively [ contraints ]. but in both cases i get after grompp: [ file info.top, line 14 ]: Atom index (6) in distance_restraints out of bounds (1-5). so i think the problem is that i have two molecules. but is there probably another way to get this work?!? thanks for an answer. thomas schlesier ___ 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] restraints or constraints over two molecules
Hi, We still need an elegant solution for this problem. Currently the only option is to merge the two moleculetype definitions into one. Or if you are also happy with an harmonic restraint, you can use the pull code. Berk. Date: Wed, 2 Apr 2008 15:53:19 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] restraints or constraints over two molecules hi, i want to ask if there is a possibility to make distance restraints or contraints over two molecules? till now i have two .itp files (one for each molecule) and i include them with 'inculde ...itp . after that i have [ system ] and [ molecules ] (with my two molecules) and then [ distance_restraints ] respectively [ contraints ]. but in both cases i get after grompp: [ file info.top, line 14 ]: Atom index (6) in distance_restraints out of bounds (1-5). so i think the problem is that i have two molecules. but is there probably another way to get this work?!? thanks for an answer. thomas schlesier ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] B factor and R factor
Hi, What do B factor and R factor mean ? And what can be indicated fome them? -- Lu Shuai ___ 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] Error gmxtest
Dear All, I have compiled fftw3_3.0.1 in a specific user directory; then configured, compiled gromacs-3.3.2 according to directions and installed it in the specific directory, all without any errors, but at the end make tests command fails, the output is: (if test -d gmxtest; then cd gmxtest; ./gmxtest.pl all; cd ..; \ else echo No gmxtest directory found. Please download and unpack it here.;\ fi) No gmxtest directory found. Please download and unpack it here. In addition, after make install the note was: Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Could you please let me know if my installation was successful despite make tests message, and what should I do about the note on PATH and MANPATH? (I do not have an extensive Linux skills, what file should I modify and how?) Thank you very much in advance! Nadia ___ 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] Error gmxtest
Nadia Gro wrote: Dear All, I have compiled fftw3_3.0.1 in a specific user directory; then configured, compiled gromacs-3.3.2 according to directions and installed it in the specific directory, all without any errors, but at the end make tests command fails, the output is: (if test -d gmxtest; then cd gmxtest; ./gmxtest.pl all; cd ..; \ else echo No gmxtest directory found. Please download and unpack it here.;\ fi) No gmxtest directory found. Please download and unpack it here. So? Do as it says... In addition, after make install the note was: Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Could you please let me know if my installation was successful despite make tests message, and what should I do about the note on PATH and MANPATH? (I do not have an extensive Linux skills, what file should I modify and how?) Probably, yes. Thank you very much in advance! Nadia ___ 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] topolbuild 1.1, update to an all-atoms model gromacs topology generator
I've made a number of changes to topolbuild to correct problems, and improve the results. Version 1.1 is now available in the user contributions at the gromacs web site. The following revisions are included: 1. Scaled Tripos out of plane bending parameter to derive better improper dihedral force field settings. 2. Corrected an error in nitrogen bond type differentiation method. 3. Corrected error in aromatic bond type differentiation. 4. Changed how charge deviations are corrected. 5. Added code to correctly add charge attributed to lone pairs in a Sybyl generated structure to the parent atom. 6. Changed non-bonded parameters output to make output for single atom ions into comments. 7. Corrected analysis of ring types. 8. Corrected determination of atom types in cases where 0 is the expected number of bound atoms, bound hydrogens, or bound electron withdrawing groups on the atom to which a hydrogen is bound. 9. Corrected antechamber tables to make CZ of arginine be assigned its correct type of CA rather than the default type of CM with the amber force fields. 10. Improved charge group number assignment. 11. Added option to produce only the coordinates (*.gro) file for those cases where one has several coordinate sets (poses) that use the same topology. 12. Included some of the required Tripos, amber, and gaff force field tables with my modifications of some of them. As with the original, the required input is a syntactically correct mol2 file with Tripos atom types. At this time, output is still limited to topologies with amber, gaff, or Tripos force fields. All options present in the prior version remain as before. The -gro option to produce only the coordinates (*.gro) file is the only option added. Because I found it necessary to alter some of the original atom type definition and parameters files, I am now including those with the program. I hope this proves useful. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. http://tc.deals.yahoo.com/tc/blockbuster/text5.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] how to calculate the RMSD of the peptide conformation relative to the NMR structure?
Dear everyone, Can somebody tell me how to calculate the RMSD of the peptide conformation relative to the NMR structure? Thanks again! Fufeng Liu ___ 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] how to calculate the RMSD of the peptide conformation relative to the NMR structure?
Quoting [EMAIL PROTECTED]: Dear everyone, Can somebody tell me how to calculate the RMSD of the peptide conformation relative to the NMR structure? Thanks again! Try g_rms -h -Justin Fufeng Liu ___ 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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] how to put two rmsd plot in one plot
Dear all, I need two rmsd plots(protein and the ligand) , and I want use one plot display them, How can I do it? Thank you in advance ___ 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] how to put two rmsd plot in one plot
Rui Li wrote: Dear all, I need two rmsd plots(protein and the ligand) , and I want use one plot display them, How can I do it? Please describe better. 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
Re: [gmx-users] how to put two rmsd plot in one plot
You mean 2 plots ? one above the other ? Or all this data on the same plot ? On Thu, Apr 3, 2008 at 1:27 AM, Mark Abraham [EMAIL PROTECTED] wrote: Rui Li wrote: Dear all, I need two rmsd plots(protein and the ligand) , and I want use one plot display them, How can I do it? Please describe better. 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 -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ 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
