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<DIV dir=ltr align=left><SPAN class=426592722-01042009><FONT face=Arial
color=#0000ff size=2>g_angle will do that fine, and with the options you used it
should have done so. Possible issue that may make that fail is you failed
to generate the correct angle index file for the dihedral(s) of
interest.</FONT></SPAN></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV><!-- Converted from text/plain format -->
<P><FONT size=2>Catch ya,<BR><BR>Dr. Dallas Warren<BR>Department of
Pharmaceutical Biology and Pharmacology<BR>Pharmacy and Pharmaceutical Sciences,
Monash University<BR>381 Royal Parade, Parkville VIC
3010<BR>dallas.warren@pharm.monash.edu.au<BR>+61 3 9903
9167<BR>---------------------------------<BR>When the only tool you own is a
hammer, every problem begins to resemble a nail.</FONT> </P>
<DIV> </DIV><BR>
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style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px solid; MARGIN-RIGHT: 0px">
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<FONT face=Tahoma size=2><B>From:</B> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <B>On Behalf Of </B>Venkat
Reddy<BR><B>Sent:</B> Wednesday, 1 April 2009 7:52 PM<BR><B>To:</B> Discussion
list for GROMACS users<BR><B>Subject:</B> Re: [gmx-users] How to calculate the
dihedral angle variations ???<BR></FONT><BR></DIV>
<DIV></DIV>Hai Sir ! <BR> Actually i want to see the dihedral angle
(Cā-S-S-Cā) variation over time.I used the commands<BR> <BR>"g_angle -f
trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od angdist.xvg -ov angaver.xvg
-of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg
-type dihedral -all"<BR><BR>"g_chi -s
gp123_full.gro -f gp123_full.trr -o order.xvg -jc Jcoupling.xvg -g chi.log
-rama -all"<BR> <BR>Please suggest me the right options<BR>Thanks for ur
concern<BR> <BR><BR>
<DIV class=gmail_quote>2009/4/1 Tsjerk Wassenaar <SPAN dir=ltr><<A
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</A>></SPAN><BR>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">Hi
Venkat,<BR><BR>What exactly do you mean with variations. Do you want to
follow the<BR>angle over time, or do you want distributions with mean and
variance<BR>estimates? g_angle and g_chi seem to be the appropriate tools.
You<BR>mention you tried all suitable options, but fail to explain what
you<BR>tried and what exactly it is you want. We need that sort
of<BR>information to be able to help you
out.<BR><BR>Cheers,<BR><BR>Tsjerk<BR><BR>2009/4/1 Venkat Reddy <<A
href="mailto:venkat4bt@gmail.com">venkat4bt@gmail.com</A>>:<BR>
<DIV>
<DIV></DIV>
<DIV class=h5>> First of all Thanks for ur reply !<BR>> I tried both
g_angle and g_chi with all suitable options, but i didn't get<BR>> the
required result.Can u plz help me in this regard ???<BR>><BR>>
2009/4/1 Antonia V. <<A
href="mailto:antonia_haha@hotmail.com">antonia_haha@hotmail.com</A>><BR>>><BR>>>
Did you try g_angle??<BR>>><BR>>> Antonia<BR>>>
________________________________<BR>>> Date: Wed, 1 Apr 2009 11:35:29
+0530<BR>>> From: <A
href="mailto:venkat4bt@gmail.com">venkat4bt@gmail.com</A><BR>>> To: <A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>>>
Subject: [gmx-users] How to calculate the dihedral angle variations
???<BR>>><BR>>> Hi Everyone !<BR>>> How can i see the
variations in the "Cā-S-S-Cā" (Disulfide bridge)<BR>>> dihedral
angle during a simulation ?????<BR>>> Thanks
in advance<BR>>><BR>>><BR>>><BR>>> Cheers
from<BR>>> Venkat Reddy Chirasani<BR>>> M.Tech
Bioinformatics<BR>>> UNIVERSITY OF HYDERABAD<BR>>><BR>>>
________________________________<BR>>> check out the rest of the
Windows LiveT. More than mail-Windows LiveT goes<BR>>> way beyond your
inbox. More than messages<BR>>>
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--<BR>> Venkat Reddy Chirasani<BR>> M.Tech Bioinformatics<BR>>
UNIVERSITY OF HYDERABAD<BR>><BR>>
_______________________________________________<BR>> gmx-users mailing
list <A
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Please search the archive at <A href="http://www.gromacs.org/search"
target=_blank>http://www.gromacs.org/search</A> before posting!<BR>>
Please don't post (un)subscribe requests to the list. Use the<BR>> www
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Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php"
target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR>><BR><BR><BR><BR>--<BR></DIV></DIV>Tsjerk
A. Wassenaar, Ph.D.<BR>Junior UD (post-doc)<BR>Biomolecular NMR, Bijvoet
Center<BR>Utrecht University<BR>Padualaan 8<BR>3584 CH Utrecht<BR>The
Netherlands<BR>P: +31-30-2539931<BR>F: +31-30-2537623<BR>
<DIV>
<DIV></DIV>
<DIV class=h5>_______________________________________________<BR>gmx-users
mailing list <A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A
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target=_blank>http://www.gromacs.org/search</A> before posting!<BR>Please
don't post (un)subscribe requests to the list. Use the<BR>www interface or
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post? Read <A href="http://www.gromacs.org/mailing_lists/users.php"
target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR></DIV></DIV></BLOCKQUOTE></DIV><BR><BR
clear=all><BR>-- <BR>Venkat Reddy Chirasani<BR>M.Tech
Bioinformatics<BR>UNIVERSITY OF HYDERABAD<BR></BLOCKQUOTE></BODY></HTML>