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: [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 7:29 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: [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 > > ----------------------------------------------------- > > _______________________________________________ > > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > > 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 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
