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??<br><br>thank you<br><br><div class="gmail_quote">On Tue, Aug 2, 2011 at 1:58 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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"><br>
<br>
Sara baretller wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
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<br>
<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<br>
On Tue, Aug 2, 2011 at 1:01 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Sara baretller wrote:<br>
<br>
I have a question about the g-hbond selection . after i typed in<br>
the g_hbond , it asked me to choose two groops and i am<br>
wondering what is difference between Protein and Protein-H ?<br>
<br>
<br>
<a href="http://www.gromacs.org/__Documentation/Terminology/__Default_Index_Groups" target="_blank">http://www.gromacs.org/__<u></u>Documentation/Terminology/__<u></u>Default_Index_Groups</a><br>
<<a href="http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups" target="_blank">http://www.gromacs.org/<u></u>Documentation/Terminology/<u></u>Default_Index_Groups</a>><br>
<br>
-Justin<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>
On Thu, Jul 14, 2011 at 11:10 PM, Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu." target="_blank">Mark.Abraham@anu.edu.</a>_<u></u>_au<br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>>> wrote:<br>
<br>
On 15/07/2011 11:48 AM, Itamar Kass wrote:<br>
<br>
Hi all,<br>
<br>
I am trying to find all possible h-bonds between chains in my<br>
complex. I am using:<br>
<br>
g_hbond_d -f system_run1_MD050_fitbb.xtc -s<br>
system_for_EM.tpr -n<br>
system.ndx -g system_run1_MD050_fitbb_Hbond_<u></u>____all.log -num<br>
system_run1_MD050_fitbb_Hbnum_<u></u>____all.xvg -hbn<br>
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)<br>
malloc:<br>
*** error for object 0xd: pointer being reallocated was not<br>
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),<br>
which I compiled myself (not via fink). I also tried to<br>
compile<br>
it using dmalloc without success.<br>
<br>
<br>
Sounds like a bug. Try g_hbond from a more recent version of<br>
GROMACS.<br>
<br>
BTW, you should only compile and use tools in double precision if<br>
that extra accuracy is what you actually need. Otherwise<br>
you're just<br>
running slower than you need to. All tools can read files<br>
written at<br>
either precision.<br>
<br>
Mark<br>
<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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