<P>
<BR>
<BR>
Thanks Justin for your valuable suggestions<BR>
I have done the way you suggested. I gave command like this<BR>
g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms) -num .xvg -hbm .xpm<BR>
it showed <BR>
Select a group: 15<BR>
Selected 15: 'MainChain+H_&_r_22_50_56_121_22'<BR>
Select a group: 15<BR>
Selected 15: 'MainChain+H_&_r_22_50_56_121_22'<BR>
Calculating hydrogen bonds in MainChain+H_&_r_22_50_56_121_22 (25 atoms)<BR>
Found 4 donors and 8 acceptors<BR>
Reading frame 0 time 0.000 <BR>
Will do grid-seach on 16x16x16 grid, rcut=0.35<BR>
Reading frame 37000 time 7400.000 <BR>
No hydrogen bonds found!!<BR>
Average number of hbonds per timeframe 0.000 out of 16 possible<BR>
<BR>
gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey)<BR>
<BR>
It displayed there is no Hydrogen bonds in selected mainchain+H residues. but it showed 4 donors and 8 acceptors, that doesnt mean that its having H-bond?<BR>
Later<BR>
when I tried to convert .xpm to .eps by using command<BR>
xpm2ps -f .xpm -o .eps it showed<BR>
Floating point exception<BR>
Can you please give me your kind suggestion<BR>
<BR>
Thanks in advance. <BR>
<BR>
On Wed, 03 Sep 2008 Justin A.Lemkul wrote :<BR>
><BR>
><BR>
>minnale wrote:<BR>
>> Hi all,<BR>
>> I am confusing while calculating hydrogen bonds of my protein.I issued this command g_hbond -f .xtc -s .tpr -num .xvg<BR>
>>I didnt mention .ndx because I wanted to know the H-bonds in whole protein system. I have selected mainchain+H two times, command went fine and it showed<BR>
>><BR>
>>Select a group: 7<BR>
>>Selected 7: 'MainChain+H'<BR>
>>Select a group: 7<BR>
>>Selected 7: 'MainChain+H'<BR>
>>Calculating hydrogen bonds in MainChain+H (881 atoms)<BR>
>>Found 170 donors and 355 acceptors<BR>
>>Reading frame 0 time 0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35<BR>
>>Reading frame 37000 time 7400.000 Average number of hbonds per timeframe 81.692 out of 30175 possible<BR>
>>gcq#295: "It Just Tastes Better" (Burger King)<BR>
>><BR>
>>It generated .xvg file and it con@ title "Hydrogen Bonds"<BR>
>>@ xaxis label "Time"<BR>
>>@ yaxis label "Number"<BR>
>>@TYPE xy<BR>
>>@ view 0.15, 0.15, 0.75, 0.85<BR>
>>@ legend on<BR>
>>@ legend box on<BR>
>>@ legend loctype view<BR>
>>@ legend 0.78, 0.8<BR>
>>@ legend length 2<BR>
>>@ s0 legend "Hydrogen bonds"<BR>
>>@ s1 legend "Pairs within 0.35 nm"<BR>
>> 0 79 674<BR>
>> 0.2 87 687<BR>
>> 0.4 80 693<BR>
>> .<BR>
>> .<BR>
>> .<BR>
>> .<BR>
>> .<BR>
>> etc<BR>
>><BR>
>>1.Could you please tell me the way I have done was correct or not?<BR>
><BR>
>For calculating H-bonds within the MainChain, yes. You have not determined all of the H-bonds in the protein, however, because you are not including side chains in the calculation.<BR>
><BR>
>>2. how can I make h-bond existence map?<BR>
><BR>
>Is g_hbond -hbm not what you want?<BR>
><BR>
>-Justin<BR>
><BR>
>>3. For this is it require to write programming or script?<BR>
>><BR>
>><BR>
>><BR>
>>Rediff Shopping <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2206641_2199021/2201650/1?PARTNER=3&OAS_QUERY=null><BR>
>><BR>
>><BR>
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>><BR>
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><BR>
>-- ========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
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