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