do you suggest any other way to find the hbond?? is the cut of distance of 3 or less something i can do in this case or not??
thank you On Tue, Aug 2, 2011 at 1:58 PM, Justin A. Lemkul <[email protected]> wrote: > > > Sara baretller wrote: > >> >> does the g_hbond work for course grained file. i tried this command and it >> gave me nothing but an error it does not matter wich selection >> >> >> > If there are no hydrogens, there is nothing for g_hbond to measure. You > need an atomistic representation such that D-H-A angles and distances can be > measured. > > -Justin > > >> On Tue, Aug 2, 2011 at 1:01 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Sara baretller wrote: >> >> I have a question about the g-hbond selection . after i typed in >> the g_hbond , it asked me to choose two groops and i am >> wondering what is difference between Protein and Protein-H ? >> >> >> http://www.gromacs.org/__**Documentation/Terminology/__** >> Default_Index_Groups<http://www.gromacs.org/__Documentation/Terminology/__Default_Index_Groups> >> <http://www.gromacs.org/**Documentation/Terminology/** >> Default_Index_Groups<http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups> >> > >> >> -Justin >> >> Thank you >> >> Specify 2 groups to analyze: >> Group 0 ( System) has 7722 elements >> Group 1 ( Protein) has 2000 elements >> Group 2 ( Protein-H) has 2000 elements >> Group 3 ( C-alpha) has 0 elements >> Group 4 ( Backbone) has 0 elements >> Group 5 ( MainChain) has 0 elements >> Group 6 ( MainChain+Cb) has 0 elements >> Group 7 ( MainChain+H) has 0 elements >> Group 8 ( SideChain) has 2000 elements >> Group 9 ( SideChain-H) has 2000 elements >> Group 10 ( Prot-Masses) has 2000 elements >> Group 11 ( non-Protein) has 5722 elements >> Group 12 ( Other) has 5722 elements >> Group 13 ( W) has 5722 elemen >> >> >> >> >> On Thu, Jul 14, 2011 at 11:10 PM, Mark Abraham >> <[email protected] >> <mailto:[email protected].**au<[email protected]> >> > >> <mailto:[email protected]._**_au >> <mailto:[email protected].**au <[email protected]>>>> >> wrote: >> >> On 15/07/2011 11:48 AM, Itamar Kass wrote: >> >> Hi all, >> >> I am trying to find all possible h-bonds between chains in >> my >> complex. I am using: >> >> g_hbond_d -f system_run1_MD050_fitbb.xtc -s >> system_for_EM.tpr -n >> system.ndx -g system_run1_MD050_fitbb_Hbond_**____all.log >> -num >> system_run1_MD050_fitbb_Hbnum_**____all.xvg -hbn >> system_run1_MD050_fitbb.xtc___**__Hbond_all.ndx >> >> and after reading 100ns the system crash and report: >> >> Reading frame 1000 time 100000.000 g_hbond_d(42677) >> malloc: >> *** error for object 0xd: pointer being reallocated was not >> allocated >> *** set a breakpoint in malloc_error_break to debug >> >> I am suing gromacs 4.0.7 (double precision) on mac (10.6.8), >> which I compiled myself (not via fink). I also tried to >> compile >> it using dmalloc without success. >> >> >> Sounds like a bug. Try g_hbond from a more recent version of >> GROMACS. >> >> BTW, you should only compile and use tools in double precision >> if >> that extra accuracy is what you actually need. Otherwise >> you're just >> running slower than you need to. All tools can read files >> written at >> either precision. >> >> Mark >> >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>**> >> >> >> >> http://lists.gromacs.org/____**mailman/listinfo/gmx-users<http://lists.gromacs.org/____mailman/listinfo/gmx-users> >> >> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> > >> >> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >> >> Please search the archive at >> >> http://www.gromacs.org/____**Support/Mailing_Lists/Search<http://www.gromacs.org/____Support/Mailing_Lists/Search> >> >> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> > >> >> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> > >> <mailto:gmx-users-request@__gr**omacs.org <http://gromacs.org> >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >>. >> >> Can't post? Read >> >> http://www.gromacs.org/____**Support/Mailing_Lists<http://www.gromacs.org/____Support/Mailing_Lists> >> >> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> > >> >> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> >> >> -- ==============================**__========== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >> ==============================**__========== >> >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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