Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL.
Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -----Original Message----- From: "Justin A. Lemkul" <[email protected]> Sender: [email protected] Date: Mon, 12 Sep 2011 07:52:54 To: Discussion list for GROMACS users<[email protected]> Reply-To: [email protected], Discussion list for GROMACS users <[email protected]> Subject: Re: [gmx-users] g_dist error aiswarya pawar wrote: > hi Justin, > > As far i referred the OW,HW1 etc are water atoms so how can it be > distance between the SOL protein atoms, instead it is SOL water atoms. > The printed distance indicates that there is a certain water molecule that is just over 2 hydrogen bonding lengths away from your protein's backbone. Sounds normal to me. -Justin > Thanks > > On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <[email protected] > <mailto:[email protected]>> wrote: > > > > aiswarya pawar wrote: > > Hi Users, > > Am using g_dist to find the distance between water and protein. > but my output has the values of SOL-water distance. > > t: 1 136 SOL 2336 OW 0.772373 (nm) > > > This is not a water-water distance, it is the output of the -dist > option telling you that water molecule 136 has its OW atom at > 0.7723273 nm from whatever your reference group is. > > -Justin > > -- > ==============================__========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin > <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================__========== > -- > gmx-users mailing list [email protected] > <mailto:[email protected]> > http://lists.gromacs.org/__mailman/listinfo/gmx-users > <http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at > http://www.gromacs.org/__Support/Mailing_Lists/Search > <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 [email protected] > <mailto:[email protected]>. > Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists> > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
