Hi, index files contain groups of atoms represented by their atom number. Just check an index file how it is constructed. By default, there are several groups (System, Protein, Protein-H, etc.). So if you want to work with a range of residues (e.g. 1-300) just create a new group and copy the atom indices of those residues (1-xxxx) from another group into it (But carefully check from which existing group you are copying, depends on what you are interested).
Best regards, Björn > "to select and copy the indices from an existing index-file to create a new > group" > > I am sorry I did not understand the meaning of the above ? I will have the > first atom number and the last atom number, and then ? How do I copy the > indices ... > > On Fri, Feb 22, 2008 at 10:58 AM, Bjoern Windshuegel > <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> wrote: Hi, > > I assume you want to select a range of residues, not some scattered amino > acids.. > So just check from your gro-file the atom numbers of begin and end of the > region you need and use the information to select and copy the indices from > an existing index-file to create a new group. > > > Best regards, > > Björn > > > Hello, > > > > I want to select 300 residues out of my 1000 residue protein and make an > > index out of it. make_ndx does not seem to have a simple method to do > > this. These are all residues in the same chain. How does one do this ? > > > > Sincerely > > > > -Maria > > > > -- > > Maria G. > > Technical University of Denmark > > Copenhagen > > -- > Dr. Björn Windshügel > > Department of Pharmaceutical Chemistry > University of Kuopio > P.O. Box 1627 > 70211 Kuopio, FINLAND > > Email: [EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]> > Phone: (+358) 17 162463 > Fax: (+358) 17 162456 > Web: > www.uku.fi/farmasia/fake/modelling/index.shtml<http://www.uku.fi/farmasia/f >ake/modelling/index.shtml> _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org<mailto: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]<mailto:[EMAIL PROTECTED]>. Can't > post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > Maria G. > Technical University of Denmark > Copenhagen -- Dr. Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: [EMAIL PROTECTED] Phone: (+358) 17 162463 Fax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtml _______________________________________________ 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
