sorry for keep spamming you...<br><br>so i make 2 groups: acceptors and donors (with their hydrogen)<br><br>I hope now i am correct! <br><br><br><div class="gmail_quote">On Sat, Jul 31, 2010 at 1:55 AM, 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;">
I didn't get why the command i propsed won't work.<br>
<br>
</blockquote>
<br></div>
Because you typed:<br>
<br>
a HO a OM a O<br>
<br>
I assumed you meant you would actually try this with make_ndx. It is wrong for several reasons, the most immediate of which is the use of "a" with atom types. To use "a" you must supply atom *names* not types. If you want to specify any selections based on types, you must provide a .tpr file as input and use "t" instead of "a."<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;">
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>
</blockquote>
<br></div>
These groups sound almost correct, but they do not correspond to what you typed before. You can't specify the hydrogen as its own group, since it won't be connected to its donor atom (O4). To specify the hydroxyl, for example, what you want is:<br>
<br>
a H2 | a O4<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 class="im">
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><div><div></div><div class="h5">
On Fri, Jul 30, 2010 at 8:19 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>
Vasilis Georgilas wrote:<br>
<br>
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 -<br>
donor - acceptor.<br>
So my index file should be in triplets, right?? this means I<br>
should type a HO a OA a O.<br>
<br>
Correct?<br>
<br>
<br>
No. The donor and acceptor groups should be separate. The geometry<br>
is easily calculated from O-H...O coordinates. You should also not<br>
have a group for just hydrogen, you need the group to contain the<br>
relevant functional group, which is the hydroxyl in this case (atoms<br>
H2 and O4 in a single group).<br>
<br>
Also note that your proposed command will not work. To select by<br>
atom type (i.e., HO, OA, and O) you need to provide a .tpr file as<br>
input to make_ndx and use "t HO" etc. Otherwise, select by atom name.<br>
<br>
-Justin<br>
<br>
<br>
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<br>
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<br>
1 PLM C5 3 0 7 CP2 1<br>
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>
<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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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<br>
<br>
<br>
-- <br>
Vasilis Georgilas<br>
LBG Patra<br>
Joint EoE Brno Coordinator<br></div>
mail: <a href="mailto:vasilis.georgilas@BEST.eu.org" target="_blank">vasilis.georgilas@BEST.eu.org</a> <mailto:<a href="mailto:vasilis.georgilas@BEST.eu.org" target="_blank">vasilis.georgilas@BEST.eu.org</a>><br>
mobile: +306973041057<br>
</blockquote>
<br><div><div></div><div class="h5">
-- <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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</div></div></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>