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 ?<br><br>Thank you <br><br>Specify 2 groups to analyze:<br>
Group 0 ( System) has 7722 elements<br>Group 1 ( Protein) has 2000 elements<br>Group 2 ( Protein-H) has 2000 elements<br>Group 3 ( C-alpha) has 0 elements<br>Group 4 ( Backbone) has 0 elements<br>
Group 5 ( MainChain) has 0 elements<br>Group 6 ( MainChain+Cb) has 0 elements<br>Group 7 ( MainChain+H) has 0 elements<br>Group 8 ( SideChain) has 2000 elements<br>Group 9 ( SideChain-H) has 2000 elements<br>
Group 10 ( Prot-Masses) has 2000 elements<br>Group 11 ( non-Protein) has 5722 elements<br>Group 12 ( Other) has 5722 elements<br>Group 13 ( W) has 5722 elemen<br><br><br><br><br>
<div class="gmail_quote">On Thu, Jul 14, 2011 at 11:10 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On 15/07/2011 11:48 AM, Itamar Kass wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi all,<br>
<br>
I am trying to find all possible h-bonds between chains in my complex. I am using:<br>
<br>
g_hbond_d -f system_run1_MD050_fitbb.xtc -s system_for_EM.tpr -n system.ndx -g system_run1_MD050_fitbb_Hbond_<u></u>all.log -num system_run1_MD050_fitbb_Hbnum_<u></u>all.xvg -hbn system_run1_MD050_fitbb.xtc_<u></u>Hbond_all.ndx<br>
<br>
and after reading 100ns the system crash and report:<br>
<br>
Reading frame 1000 time 100000.000 g_hbond_d(42677) malloc: *** error for object 0xd: pointer being reallocated was not allocated<br>
*** set a breakpoint in malloc_error_break to debug<br>
<br>
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.<br>
</blockquote>
<br></div>
Sounds like a bug. Try g_hbond from a more recent version of GROMACS.<br>
<br>
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.<br>
<font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
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