I didn't get why the command i propsed won't work.<br><br>My idea, according what you proposed, is to use make_ndx and then make 3 groups:<br><br>oxygen with the doble bond, oxyegn of carboxyle and hydroxele<br><br>
and then with the g_hbond to do all the calculations.<br><br>Right??<br><br>thank you once again for the help<br><br><div class="gmail_quote">On Fri, Jul 30, 2010 at 8:19 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>
Vasilis Georgilas wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
This is from my topology file for palmitic acid.<br>
<br>
You say a should make a group of all O, of OM and of HO.<br>
<br>
But for the calculation I need the angle between hydrogene - donor - acceptor.<br>
So my index file should be in triplets, right?? this means I should type a HO a OA a O.<br>
<br>
Correct?<br>
<br>
</blockquote>
<br></div>
No. The donor and acceptor groups should be separate. The geometry is easily calculated from O-H...O coordinates. You should also not have a group for just hydrogen, you need the group to contain the relevant functional group, which is the hydroxyl in this case (atoms H2 and O4 in a single group).<br>
<br>
Also note that your proposed command will not work. To select by atom type (i.e., HO, OA, and O) you need to provide a .tpr file as input to make_ndx and use "t HO" etc. Otherwise, select by atom name.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
thank you<br>
<br>
<br>
[ atoms ]<br>
; nr type resnr residu atom cgnr charge 1 HO 1 PLM H2 1 0.370 2 OM 1 PLM O4 1 -0.460 3 C 1 PLM C3 1 0.42 4 O 1 PLM O5 1 -0.45 5 CP2 1 PLM C4 2 0.12 6 CP2 1 PLM C5 3 0 7 CP2 1 PLM C6 4 0 8 CP2 1 PLM C7 5 0<br>
9 CP2 1 PLM C8 6 0<br>
10 CP2 1 PLM C9 7 0<br>
11 CP2 1 PLM C10 8 0<br>
12 CP2 1 PLM C11 9 0<br>
13 CP2 1 PLM C12 10 0<br>
14 CP2 1 PLM C13 11 0<br>
15 CP2 1 PLM C14 12 0<br>
16 CP2 1 PLM C15 13 0<br>
17 CP2 1 PLM C16 14 0<br>
18 CP2 1 PLM C17 15 0<br>
19 CP3 1 PLM C18 16 0<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Vasilis Georgilas<br>LBG Patra<br>Joint EoE Brno Coordinator<br>mail: <a href="mailto:vasilis.georgilas@BEST.eu.org">vasilis.georgilas@BEST.eu.org</a><br>mobile: +306973041057<br>