Justin Lemkul wrote > On 4/3/13 11:13 AM, Oleksandr Sushko wrote: >> Dear Gromacs users, >> can you help me please with next issue: >> I'm analysing solvation shell of water molecules around a protein. >> I use g_select to select different layers of water based on distance >> criteria. >> The output index file contains all the atoms which satisfy the specified >> criteria. >> For some molecules on the edge only some atoms are within the specified >> distance >> from protein. >> So some molecules in the selection are represented only by 1 or 2 atoms >> out of 3. >> >> Such selection works fine for example for g_hbond, but it does not work >> for >> g_dipoles. >> The error in case of g_dipoles is: "index group is not a set of whole >> molecules" >> >> is there a smart way (except manual editing of .ndx file) to select the >> whole >> molecules within some distance from protein (with COM within specified >> distance >> from protein surface)? >> > > It would help to know exactly what your selection syntax was. I think you > can > use something like "same residue as (within ...)" for your selection, but > I > haven't tried it. > > -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@ > 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-request@ > . > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Thanks a lot, now I used: 'group "SOL" and same residue as within ... of group "Protein"' and it selected the whole water molecules as I wanted. cheers, Oleksandr -- View this message in context: http://gromacs.5086.n6.nabble.com/g-dipoles-index-group-is-not-a-set-of-the-whole-molecules-tp5006886p5006933.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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