[gmx-users] make_ndx

[David van der Spoel]

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: mn2 at hw.ac.uk
> Phone: +44(0)1314518265
> Fax : +44(0) 131 451 3009
> 
> 
> 
> 
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 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: mn2 at hw.ac.uk
>  > Phone: +44(0)1314518265
>  > Fax : +44(0) 131 451 3009
>  >
>  >
>  >
>  >
>  >
>  >
>  > -----Original Message-----
>  > From: gmx-users-bounces at gromacs.org 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" <mn2 at hw.ac.uk> 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: mn2 at hw.ac.uk
>  >  > 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
> spoel at xray.bmc.uu.se    spoel at gromacs.org   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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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