[gmx-users] make_ndx
Naser, Md Abu
mn2 at hw.ac.uk
Thu Sep 27 08:51:44 CEST 2007
Thanks XAvier and David!
I think I know what I need to do to
get my 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 David van der Spoel
Sent: Thu 27/09/2007 7:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx
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
> > -----------------------------------------------------
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070927/b17c95ed/attachment.html>
More information about the gromacs.org_gmx-users
mailing list