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<P><FONT SIZE=2>Thanks XAvier and David!<BR>
I think I know what I need to do to<BR>
get my group.<BR>
<BR>
With regards,<BR>
<BR>
Abu Naser<BR>
<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Fax : +44(0) 131 451 3009<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of David van der Spoel<BR>
Sent: Thu 27/09/2007 7:29 AM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] make_ndx<BR>
<BR>
Naser, Md Abu wrote:<BR>
> Thanks david!<BR>
><BR>
oops I misread. Sidechains do not contain C-alpha (which you can easily<BR>
check in the index file).<BR>
So within make_ndx type h for help on joining the two.<BR>
<BR>
><BR>
><BR>
> Abu Naser<BR>
><BR>
> School Of Life Sciences<BR>
> Heriot-Watt University<BR>
> Edinburgh EH14 4AS<BR>
> Email: mn2@hw.ac.uk<BR>
> Phone: +44(0)1314518265<BR>
> Fax : +44(0) 131 451 3009<BR>
><BR>
><BR>
><BR>
><BR>
><BR>
><BR>
> -----Original Message-----<BR>
> From: gmx-users-bounces@gromacs.org on behalf of David van der Spoel<BR>
> Sent: Thu 27/09/2007 7:17 AM<BR>
> To: Discussion list for GROMACS users<BR>
> Subject: Re: [gmx-users] make_ndx<BR>
><BR>
> Naser, Md Abu wrote:<BR>
> > Hi XAvier,<BR>
> ><BR>
> > "Single out" I mean pick up only the side chain bonded with alpha<BR>
> > carbon atom and<BR>
> > put them in a group using make_ndx.<BR>
> ><BR>
> all side chains are.<BR>
> and sidechain is a default group.<BR>
><BR>
> > With regards,<BR>
> ><BR>
> ><BR>
> > Abu Naser<BR>
> ><BR>
> > School Of Life Sciences<BR>
> > Heriot-Watt University<BR>
> > Edinburgh EH14 4AS<BR>
> > Email: mn2@hw.ac.uk<BR>
> > Phone: +44(0)1314518265<BR>
> > Fax : +44(0) 131 451 3009<BR>
> ><BR>
> ><BR>
> ><BR>
> ><BR>
> ><BR>
> ><BR>
> > -----Original Message-----<BR>
> > From: gmx-users-bounces@gromacs.org on behalf of Xavier Periole<BR>
> > Sent: Wed 26/09/2007 8:42 PM<BR>
> > To: Discussion list for GROMACS users<BR>
> > Subject: Re: [gmx-users] make_ndx<BR>
> ><BR>
> > On Wed, 26 Sep 2007 20:08:06 +0100<BR>
> > "Naser, Md Abu" <mn2@hw.ac.uk> wrote:<BR>
> > > Hi All User,<BR>
> > ><BR>
> > > Is there anyway I can single out side chain of alpha carbon atom using<BR>
> > >make_ndx?<BR>
> ><BR>
> > What do you mean by "single out"<BR>
> > and with "side chain of alpha carbon" ?<BR>
> ><BR>
> > ><BR>
> > > Thanks in advance.<BR>
> > ><BR>
> > > Abu Naser<BR>
> > ><BR>
> > > School Of Life Sciences<BR>
> > > Heriot-Watt University<BR>
> > > Edinburgh EH14 4AS<BR>
> > > Email: mn2@hw.ac.uk<BR>
> > > Phone: +44(0)1314518265<BR>
> > >Fax : +44(0) 131 451 3009<BR>
> > ><BR>
> > ><BR>
> > ><BR>
> > ><BR>
> ><BR>
> > -----------------------------------------------------<BR>
> > XAvier Periole - PhD<BR>
> ><BR>
> > 1- Institute of Molecular Assemblies<BR>
> > City University of New York - USA<BR>
> > 2- Molecular Dynamics-Group<BR>
> > University of Groningen - The Netherlands<BR>
> > <A HREF="http://md.chem.rug.nl/~periole">http://md.chem.rug.nl/~periole</A><BR>
> > -----------------------------------------------------<BR>
> > _______________________________________________<BR>
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> posting!<BR>
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> ><BR>
> ><BR>
> > ------------------------------------------------------------------------<BR>
> ><BR>
> > _______________________________________________<BR>
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><BR>
><BR>
> --<BR>
> David.<BR>
> ________________________________________________________________________<BR>
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>
> Dept. of Cell and Molecular Biology, Uppsala University.<BR>
> Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
> phone: 46 18 471 4205 fax: 46 18 511 755<BR>
> spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A><BR>
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><BR>
> _______________________________________________<BR>
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> Please don't post (un)subscribe requests to the list. Use the<BR>
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<BR>
<BR>
--<BR>
David.<BR>
________________________________________________________________________<BR>
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>
Dept. of Cell and Molecular Biology, Uppsala University.<BR>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
phone: 46 18 471 4205 fax: 46 18 511 755<BR>
spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A><BR>
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Please search the archive at <A HREF="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<BR>
Please don't post (un)subscribe requests to the list. Use the<BR>
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