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 ?
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 <mark.abra...@anu.edu.au>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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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