<P>
<BR>
Thanks for your reply David<BR>
Yesterday I have issued the command like this<BR>
g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -g .log it has showed that invalid command line argument -g and got answer from archives that I am using gromacs version 3.3.1 but -g flag I can use for version recent versions. <BR>
Is there anyway to get .log file using with gromacs 3.3.1<BR>
<BR>
On Fri, 29 Aug 2008 gmx-users-request@gromacs.org wrote :<BR>
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>Today's Topics:<BR>
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> 1. Re: Re: [gmx-users] g_hbond + invalid command line argument<BR>
> -g (minnale )<BR>
> 2. a question about the content in atm-pair.out file (Cao, Yang)<BR>
> 3. about connections (ravi sharma)<BR>
> 4. Re: g_hbond + invalid command line argument -g<BR>
> (David van der Spoel)<BR>
><BR>
><BR>
>----------------------------------------------------------------------<BR>
><BR>
>Message: 1<BR>
>Date: 29 Aug 2008 04:48:02 -0000<BR>
> From: "minnale " <minnale_gnos@rediffmail.com><BR>
>Subject: Re: Re: [gmx-users] g_hbond + invalid command line argument<BR>
> -g<BR>
>To: "gmx-users1" <gmx-users@gromacs.org><BR>
>Message-ID: <20080829044802.3682.qmail@f5mail-237-208.rediffmail.com><BR>
>Content-Type: text/plain; charset="iso-8859-1"<BR>
><BR>
><BR>
>Thanks Justin for your reply<BR>
>I am interested to get file which contain how many hydrogen bonds are there in my protein and the bonds present between which atoms?<BR>
>Is there anyway to get this file<BR>
>can you please tell me,<BR>
>Thanks in advance for your kind suggestion<BR>
><BR>
>On Thu, 28 Aug 2008 Justin A.Lemkul wrote :<BR>
> ><BR>
> ><BR>
> >minnale wrote:<BR>
> >><BR>
> >>Thanks Justin for your quick reply<BR>
> >>the g_hbond command ran succesfully and gave me .xvg file and it contain 3 columns<BR>
> >>that is like<BR>
> >><BR>
> >>@ title "Hydrogen Bonds"<BR>
> >>@ xaxis label "Time"<BR>
> >>@ yaxis label "Number"<BR>
> >>@TYPE xy<BR>
> >>@ view 0.15, 0.15, 0.75, 0.85<BR>
> >>@ legend on<BR>
> >>@ legend box on<BR>
> >>@ legend loctype view<BR>
> >>@ legend 0.78, 0.8<BR>
> >>@ legend length 2<BR>
> >>@ s0 legend "Hydrogen bonds"<BR>
> >>@ s1 legend "Pairs within 0.35 nm"<BR>
> >> 0 79 674<BR>
> >> 0.2 87 687<BR>
> >> 0.4 80 693<BR>
> >> 0.6 69 690<BR>
> >> 0.8 79 691<BR>
> >> 1 74 690<BR>
> >> 1.2 81 700<BR>
> >> 1.4 75 681<BR>
> >> 1.6 83 687<BR>
> >><BR>
> >>the first column is time then could please tell about 2nd and 3rd columns<BR>
> >>Thanks in advance.<BR>
> ><BR>
> >Read the header of the file, specifically:<BR>
> ><BR>
> >@ s0 legend "Hydrogen bonds"<BR>
> >@ s1 legend "Pairs within 0.35 nm"<BR>
> ><BR>
> >Gromacs always prints legends for what the data mean.<BR>
> ><BR>
> >-Justin<BR>
> ><BR>
> >><BR>
> >>On Thu, 28 Aug 2008 Justin A.Lemkul wrote :<BR>
> >> ><BR>
> >> ><BR>
> >> >minnale wrote:<BR>
> >> >> Hi all,<BR>
> >> >> I am new to gromacs, I am interested in calculate Hydrogen bonds of my protein. So I have issued the *g_hbond command like this<BR>
> >> >>g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues mainchain+H atoms) -num .xvg -g .log<BR>
> >> >>its showed<BR>
> >> >><BR>
> >> >>Program g_hbond, VERSION 3.3.1<BR>
> >> >>Source code file: statutil.c, line: 799<BR>
> >> >><BR>
> >> >>Invalid command line argument:<BR>
> >> >>-g<BR>
> >> >><BR>
> >> >>Can you please tell where I have done mistake?<BR>
> >> >>Thanks in advance for your valuable suggestions.<BR>
> >> >><BR>
> >> >><BR>
> >> ><BR>
> >> >The error tells you exactly what the problem is. There is no such option. The -g flag appears in newer versions of Gromacs.<BR>
> >> ><BR>
> >> >-Justin<BR>
> >> ><BR>
> >> >><BR>
> >> >><BR>
> >> >>------------------------------------------------------------------------<BR>
> >> >><BR>
> >> >>_______________________________________________<BR>
> >> >>gmx-users mailing list gmx-users@gromacs.org<BR>
> >> >>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
> >> >>Please search the archive at http://www.gromacs.org/search before posting!<BR>
> >> >>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org.<BR>
> >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
> >> ><BR>
> >> >-- ========================================<BR>
> >> ><BR>
> >> >Justin A. Lemkul<BR>
> >> >Graduate Research Assistant<BR>
> >> >Department of Biochemistry<BR>
> >> >Virginia Tech<BR>
> >> >Blacksburg, VA<BR>
> >> >jalemkul[at]vt.edu | (540) 231-9080<BR>
> >> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
> >> ><BR>
> >> >========================================<BR>
> >><BR>
> >><BR>
> >><BR>
> >><BR>
> >>------------------------------------------------------------------------<BR>
> >><BR>
> >>_______________________________________________<BR>
> >>gmx-users mailing list gmx-users@gromacs.org<BR>
> >>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
> >>Please search the archive at http://www.gromacs.org/search before posting!<BR>
> >>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org.<BR>
> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
> ><BR>
> >-- ========================================<BR>
> ><BR>
> >Justin A. Lemkul<BR>
> >Graduate Research Assistant<BR>
> >Department of Biochemistry<BR>
> >Virginia Tech<BR>
> >Blacksburg, VA<BR>
> >jalemkul[at]vt.edu | (540) 231-9080<BR>
> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
> ><BR>
> >========================================<BR>
>-------------- next part --------------<BR>
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><BR>
>------------------------------<BR>
><BR>
>Message: 2<BR>
>Date: Fri, 29 Aug 2008 00:19:33 -0500<BR>
> From: "Cao, Yang" <yang.cao@ttu.edu><BR>
>Subject: [gmx-users] a question about the content in atm-pair.out file<BR>
>To: "gmx-users@gromacs.org" <gmx-users@gromacs.org><BR>
>Cc: "Hase, Bill" <bill.hase@ttu.edu><BR>
>Message-ID: <E173365B57CAD5458AB0D1AABD88ACE14C10BBB3E7@CRIUS.ttu.edu><BR>
>Content-Type: text/plain; charset="iso-8859-1"<BR>
><BR>
>Hello all,<BR>
>Sorry to bother you, I have a question about the content in the file atm-pair.out file which is generated by the command g_mindist. Here is several lines of the file:<BR>
>"<BR>
><BR>
>0.000000e+00 114 72<BR>
><BR>
>1.000000e+01 114 72<BR>
><BR>
>2.000000e+01 85 66<BR>
><BR>
>3.000000e+01 85 65<BR>
><BR>
>4.000000e+01 82 66<BR>
><BR>
>5.000000e+01 111 71"<BR>
><BR>
><BR>
><BR>
>the first column is the time but I am not sure about the next two columns, Are they the number of atoms in each group which are caculated during the process?<BR>
><BR>
><BR>
><BR>
>Best wishes?<BR>
><BR>
><BR>
>Department of Chemistry and Biochemistry<BR>
>Tesax Tech University<BR>
>Lubbock, TX 79409<BR>
><BR>
><BR>
>------------------------------<BR>
><BR>
>Message: 3<BR>
>Date: Thu, 28 Aug 2008 23:24:50 -0700 (PDT)<BR>
> From: ravi sharma <rdsharma_4u@yahoo.com><BR>
>Subject: [gmx-users] about connections<BR>
>To: gmx-users@gromacs.org<BR>
>Message-ID: <23975.21952.qm@web50609.mail.re2.yahoo.com><BR>
>Content-Type: text/plain; charset="utf-8"<BR>
><BR>
>hello guys,<BR>
>Â<BR>
>is there any idea how to extract no. of connections from trejectory....................?<BR>
><BR>
><BR>
><BR>
>Ravi Datta Sharma<BR>
>Lecturer,<BR>
>Bioinformatics,<BR>
>Department of Microbiology,<BR>
>CCS Unversity,<BR>
>Meerut<BR>
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â<BR>
><BR>
><BR>
><BR>
> Check out the all-new face of Yahoo! India. Go to http://in.yahoo.com/<BR>
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><BR>
>------------------------------<BR>
><BR>
>Message: 4<BR>
>Date: Fri, 29 Aug 2008 08:44:31 +0200<BR>
> From: David van der Spoel <spoel@xray.bmc.uu.se><BR>
>Subject: Re: [gmx-users] g_hbond + invalid command line argument -g<BR>
>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>
>Message-ID: <48B79ACF.8050807@xray.bmc.uu.se><BR>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<BR>
><BR>
>minnale wrote:<BR>
> ><BR>
> > Thanks Justin for your reply<BR>
> > I am interested to get file which contain how many hydrogen bonds are<BR>
> > there in my protein and the bonds present between which atoms?<BR>
> > Is there anyway to get this file<BR>
> > can you please tell me,<BR>
><BR>
>g_hbond -h<BR>
><BR>
> > Thanks in advance for your kind suggestion<BR>
> ><BR>
> > On Thu, 28 Aug 2008 Justin A.Lemkul wrote :<BR>
> > ><BR>
> > ><BR>
> > >minnale wrote:<BR>
> > >><BR>
> > >>Thanks Justin for your quick reply<BR>
> > >>the g_hbond command ran succesfully and gave me .xvg file and it<BR>
> > contain 3 columns<BR>
> > >>that is like<BR>
> > >><BR>
> > >>@ title "Hydrogen Bonds"<BR>
> > >>@ xaxis label "Time"<BR>
> > >>@ yaxis label "Number"<BR>
> > >>@TYPE xy<BR>
> > >>@ view 0.15, 0.15, 0.75, 0.85<BR>
> > >>@ legend on<BR>
> > >>@ legend box on<BR>
> > >>@ legend loctype view<BR>
> > >>@ legend 0.78, 0.8<BR>
> > >>@ legend length 2<BR>
> > >>@ s0 legend "Hydrogen bonds"<BR>
> > >>@ s1 legend "Pairs within 0.35 nm"<BR>
> > >> 0 79 674<BR>
> > >> 0.2 87 687<BR>
> > >> 0.4 80 693<BR>
> > >> 0.6 69 690<BR>
> > >> 0.8 79 691<BR>
> > >> 1 74 690<BR>
> > >> 1.2 81 700<BR>
> > >> 1.4 75 681<BR>
> > >> 1.6 83 687<BR>
> > >><BR>
> > >>the first column is time then could please tell about 2nd and 3rd columns<BR>
> > >>Thanks in advance.<BR>
> > ><BR>
> > >Read the header of the file, specifically:<BR>
> > ><BR>
> > >@ s0 legend "Hydrogen bonds"<BR>
> > >@ s1 legend "Pairs within 0.35 nm"<BR>
> > ><BR>
> > >Gromacs always prints legends for what the data mean.<BR>
> > ><BR>
> > >-Justin<BR>
> > ><BR>
> > >><BR>
> > >>On Thu, 28 Aug 2008 Justin A.Lemkul wrote :<BR>
> > >> ><BR>
> > >> ><BR>
> > >> >minnale wrote:<BR>
> > >> >> Hi all,<BR>
> > >> >> I am new to gromacs, I am interested in calculate Hydrogen<BR>
> > bonds of my protein. So I have issued the *g_hbond command like this<BR>
> > >> >>g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues<BR>
> > mainchain+H atoms) -num .xvg -g .log<BR>
> > >> >>its showed<BR>
> > >> >><BR>
> > >> >>Program g_hbond, VERSION 3.3.1<BR>
> > >> >>Source code file: statutil.c, line: 799<BR>
> > >> >><BR>
> > >> >>Invalid command line argument:<BR>
> > >> >>-g<BR>
> > >> >><BR>
> > >> >>Can you please tell where I have done mistake?<BR>
> > >> >>Thanks in advance for your valuable suggestions.<BR>
> > >> >><BR>
> > >> >><BR>
> > >> ><BR>
> > >> >The error tells you exactly what the problem is. There is no such<BR>
> > option. The -g flag appears in newer versions of Gromacs.<BR>
> > >> ><BR>
> > >> >-Justin<BR>
> > >> ><BR>
> > >> >><BR>
> > >> >><BR>
> > >><BR>
> > >>------------------------------------------------------------------------<BR>
> > >> >><BR>
> > >> >>_______________________________________________<BR>
> > >> >>gmx-users mailing list gmx-users@gromacs.org<BR>
> > >> >>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
> > >> >>Please search the archive at http://www.gromacs.org/search before<BR>
> > posting!<BR>
> > >> >>Please don't post (un)subscribe requests to the list. Use the www<BR>
> > interface or send it to gmx-users-request@gromacs.org.<BR>
> > >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
> > >> ><BR>
> > >> >-- ========================================<BR>
> > >> ><BR>
> > >> >Justin A. Lemkul<BR>
> > >> >Graduate Research Assistant<BR>
> > >> >Department of Biochemistry<BR>
> > >> >Virginia Tech<BR>
> > >> >Blacksburg, VA<BR>
> > >> >jalemkul[at]vt.edu | (540) 231-9080<BR>
> > >> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
> > >> ><BR>
> > >> >========================================<BR>
> > >><BR>
> > >><BR>
> > >><BR>
> > >><BR>
> > >>------------------------------------------------------------------------<BR>
> > >><BR>
> > >>_______________________________________________<BR>
> > >>gmx-users mailing list gmx-users@gromacs.org<BR>
> > >>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
> > >>Please search the archive at http://www.gromacs.org/search before<BR>
> > posting!<BR>
> > >>Please don't post (un)subscribe requests to the list. Use the www<BR>
> > interface or send it to gmx-users-request@gromacs.org.<BR>
> > >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
> > ><BR>
> > >-- ========================================<BR>
> > ><BR>
> > >Justin A. Lemkul<BR>
> > >Graduate Research Assistant<BR>
> > >Department of Biochemistry<BR>
> > >Virginia Tech<BR>
> > >Blacksburg, VA<BR>
> > >jalemkul[at]vt.edu | (540) 231-9080<BR>
> > >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
> > ><BR>
> > >========================================<BR>
> ><BR>
> ><BR>
> ><BR>
> > Rediff Shopping<BR>
> > <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2206641_2199021/2201649/1?PARTNER=3&OAS_QUERY=null><BR>
> ><BR>
> ><BR>
> > ------------------------------------------------------------------------<BR>
> ><BR>
> > _______________________________________________<BR>
> > gmx-users mailing list gmx-users@gromacs.org<BR>
> > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
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><BR>
><BR>
>--<BR>
>David van der Spoel, Ph.D., Professor of Biology<BR>
>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<BR>
>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<BR>
>spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<BR>
><BR>
><BR>
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><BR>
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>End of gmx-users Digest, Vol 52, Issue 118<BR>
>******************************************<BR>
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