Iam -dist option because I need the distance between two groups, excluding -dist gives me X,Y,Z output which I don't want. And am not specifying an -o.
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -----Original Message----- From: "Justin A. Lemkul" <jalem...@vt.edu> Date: Mon, 12 Sep 2011 22:35:28 To: <aiswarya.pa...@gmail.com>; Discussion list for GROMACS users<gmx-users@gromacs.org> Reply-To: jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com wrote: > 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. > > As was suggested several messages ago, please do NOT combine -o and -dist. If you want to measure a distance, use -o. If you want g_dist to print a list of atoms that satisfy some given criteria, use -dist, but not together. -Justin > Thanks > Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! > > -----Original Message----- > From: "Justin A. Lemkul" <jalem...@vt.edu> > Sender: gmx-users-boun...@gromacs.org > Date: Mon, 12 Sep 2011 07:52:54 > To: Discussion list for GROMACS users<gmx-users@gromacs.org> > Reply-To: jalem...@vt.edu, > Discussion list for GROMACS users <gmx-users@gromacs.org> > 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 <jalem...@vt.edu >> <mailto:jalem...@vt.edu>> 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> 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 ========================================
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