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 <jalem...@vt.edu
<mailto:jalem...@vt.edu>> 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>
-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
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au
<mailto: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
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--
==============================__==========
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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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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
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