[gmx-users] make_ndx

[Xavier Periole]

On Thu, 27 Sep 2007 07:08:00 +0100
  "Naser, Md Abu" <mn2 at hw.ac.uk> 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.

What about joining the groups "C-alpha" and "SideChain" using:
X | Y ; where X and Y are the numbers corresponding to the
groups.
Note that the C-beta is not included in the sidechain group.
you can add them by using something like:
a CB; which will create a new group.

This should be enough for you to get what you like.

> 
> 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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-----------------------------------------------------
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
-----------------------------------------------------