Hi, A general note: make_ndx and index files are not magical in any way. You can usually construct an index group from e.g. a pdb file with awk. It's just lists of atom indices.
Best, Erik 28 nov 2012 kl. 22.33 skrev Justin Lemkul: > > > On 11/28/12 3:43 PM, Hovakim Grabski wrote: >> Dear Gromacs users, >> I set a simulation of 26 base pairs of DNA with Ethidium Bromide for 5 ns. >> After a while Thymine rotated for about 70 degrees and then returned to its >> initial position. >> I wanted to find out hbonds between Adenine and Thymine but with make_ndx >> things don't work so well. >> How can I select Adenine from one strand and Thymine from the other strand >> and then run g_hbond ? > > You can use make_ndx to select any residues you want. You'll have to > describe exactly what you did that produced insufficient results. Saying it > didn't work well doesn't tell us anything, because it is in fact quite easy > to produce usable index groups. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
