Hi, I have had used 5.0 beta version and as far as I know, "gmx gangle" supports the output from g_select.
On Wed, Dec 18, 2013 at 6:39 AM, Justin Lemkul <[email protected]> wrote: > > > On 12/17/13 7:43 PM, [email protected] wrote: > >> Thanks Justin, >> >> I have tried this and I can a new index file that has an item for each >> frame with atoms that match the selection. How do I create a single index >> item and combine it into the main index file for use with other tools such >> as g_hbond? >> >> > The output of g_select is not fully compatible with any Gromacs tool, at > least in any pre-5.0 version. Given that I have had not had time yet to > fully investigate the current beta, hopefully someone else can say whether > or not the g_select output is now fully supported by other tools. > > -Justin > > > Best wishes >> James >> >> On 18 Dec 2013, at 00:14, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 12/17/13 1:55 PM, [email protected] wrote: >>> >>>> I think g_select does something like this. I am trying to do something >>>> similar: make a selection of water within 5A or so of a residue in my >>>> protein. Also need help please. >>>> >>> >>> The examples at the end of g_select -select 'help all' pretty well cover >>> most of these situations. What have you tried? What has it given you? >>> Something like: >>> >>> same residue as resname SOL and within 0.5 of residue X >>> >>> provided that residue X is defined within an .ndx file provided on the >>> command, line should work. Disclaimer: this is just off the cuff, but >>> probably pretty close. >>> >>> -Justin >>> >>> Dear Gmx Users, >>>>> >>>>> I have my carbon nanotube (lenght z axis) with proteins attached to >>>>> it. I >>>>> wish to collect RDF of given type of amino acids away from the surface >>>>> in >>>>> two dimensions (xy). Z axis does not interest me. That would make a >>>>> circle >>>>> then. My question: how to make a specific index group of this circle? >>>>> Any >>>>> ideas appreciated. >>>>> >>>>> Steven >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send >>>>> a mail to [email protected]. >>>>> >>>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> [email protected] | (410) 706-7441 >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/ >>> Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to [email protected]. >>> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (410) 706-7441 > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
