[gmx-users] malloc on mac
Sara baretller
sarabiocomputation at gmail.com
Tue Aug 2 20:04:32 CEST 2011
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 <jalemkul at vt.edu> 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 <jalemkul at vt.edu<mailto:
>> jalemkul at 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>
>> <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.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.**au<Mark.Abraham at anu.edu.au>
>> >
>> <mailto:Mark.Abraham at anu.edu._**_au
>> <mailto:Mark.Abraham at anu.edu.**au <Mark.Abraham at 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://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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