[gmx-users] Re: gmx-users Digest, Vol 52, Issue 118
minnale
minnale_gnos at rediffmail.com
Fri Aug 29 11:06:27 CEST 2008
Thanks for your reply David
Yesterday I have issued the command like this
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.
Is there anyway to get .log file using with gromacs 3.3.1
On Fri, 29 Aug 2008 gmx-users-request at gromacs.org wrote :
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>Today's Topics:
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> 1. Re: Re: [gmx-users] g_hbond + invalid command line argument
> -g (minnale )
> 2. a question about the content in atm-pair.out file (Cao, Yang)
> 3. about connections (ravi sharma)
> 4. Re: g_hbond + invalid command line argument -g
> (David van der Spoel)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: 29 Aug 2008 04:48:02 -0000
> From: "minnale " <minnale_gnos at rediffmail.com>
>Subject: Re: Re: [gmx-users] g_hbond + invalid command line argument
> -g
>To: "gmx-users1" <gmx-users at gromacs.org>
>Message-ID: <20080829044802.3682.qmail at f5mail-237-208.rediffmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>
>Thanks Justin for your reply
>I am interested to get file which contain how many hydrogen bonds are there in my protein and the bonds present between which atoms?
>Is there anyway to get this file
>can you please tell me,
>Thanks in advance for your kind suggestion
>
>On Thu, 28 Aug 2008 Justin A.Lemkul wrote :
> >
> >
> >minnale wrote:
> >>
> >>Thanks Justin for your quick reply
> >>the g_hbond command ran succesfully and gave me .xvg file and it contain 3 columns
> >>that is like
> >>
> >>@ title "Hydrogen Bonds"
> >>@ xaxis label "Time"
> >>@ yaxis label "Number"
> >>@TYPE xy
> >>@ view 0.15, 0.15, 0.75, 0.85
> >>@ legend on
> >>@ legend box on
> >>@ legend loctype view
> >>@ legend 0.78, 0.8
> >>@ legend length 2
> >>@ s0 legend "Hydrogen bonds"
> >>@ s1 legend "Pairs within 0.35 nm"
> >> 0 79 674
> >> 0.2 87 687
> >> 0.4 80 693
> >> 0.6 69 690
> >> 0.8 79 691
> >> 1 74 690
> >> 1.2 81 700
> >> 1.4 75 681
> >> 1.6 83 687
> >>
> >>the first column is time then could please tell about 2nd and 3rd columns
> >>Thanks in advance.
> >
> >Read the header of the file, specifically:
> >
> >@ s0 legend "Hydrogen bonds"
> >@ s1 legend "Pairs within 0.35 nm"
> >
> >Gromacs always prints legends for what the data mean.
> >
> >-Justin
> >
> >>
> >>On Thu, 28 Aug 2008 Justin A.Lemkul wrote :
> >> >
> >> >
> >> >minnale wrote:
> >> >> Hi all,
> >> >> 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
> >> >>g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues mainchain+H atoms) -num .xvg -g .log
> >> >>its showed
> >> >>
> >> >>Program g_hbond, VERSION 3.3.1
> >> >>Source code file: statutil.c, line: 799
> >> >>
> >> >>Invalid command line argument:
> >> >>-g
> >> >>
> >> >>Can you please tell where I have done mistake?
> >> >>Thanks in advance for your valuable suggestions.
> >> >>
> >> >>
> >> >
> >> >The error tells you exactly what the problem is. There is no such option. The -g flag appears in newer versions of Gromacs.
> >> >
> >> >-Justin
> >> >
> >> >>
> >> >>
> >> >>------------------------------------------------------------------------
> >> >>
> >> >>_______________________________________________
> >> >>gmx-users mailing list gmx-users at gromacs.org
> >> >>http://www.gromacs.org/mailman/listinfo/gmx-users
> >> >>Please search the archive at http://www.gromacs.org/search before posting!
> >> >>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >> >
> >> >-- ========================================
> >> >
> >> >Justin A. Lemkul
> >> >Graduate Research Assistant
> >> >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 at gromacs.org
> >>http://www.gromacs.org/mailman/listinfo/gmx-users
> >>Please search the archive at http://www.gromacs.org/search before posting!
> >>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >-- ========================================
> >
> >Justin A. Lemkul
> >Graduate Research Assistant
> >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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>------------------------------
>
>Message: 2
>Date: Fri, 29 Aug 2008 00:19:33 -0500
> From: "Cao, Yang" <yang.cao at ttu.edu>
>Subject: [gmx-users] a question about the content in atm-pair.out file
>To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>Cc: "Hase, Bill" <bill.hase at ttu.edu>
>Message-ID: <E173365B57CAD5458AB0D1AABD88ACE14C10BBB3E7 at CRIUS.ttu.edu>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hello all,
>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:
>"
>
>0.000000e+00 114 72
>
>1.000000e+01 114 72
>
>2.000000e+01 85 66
>
>3.000000e+01 85 65
>
>4.000000e+01 82 66
>
>5.000000e+01 111 71"
>
>
>
>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?
>
>
>
>Best wishes?
>
>
>Department of Chemistry and Biochemistry
>Tesax Tech University
>Lubbock, TX 79409
>
>
>------------------------------
>
>Message: 3
>Date: Thu, 28 Aug 2008 23:24:50 -0700 (PDT)
> From: ravi sharma <rdsharma_4u at yahoo.com>
>Subject: [gmx-users] about connections
>To: gmx-users at gromacs.org
>Message-ID: <23975.21952.qm at web50609.mail.re2.yahoo.com>
>Content-Type: text/plain; charset="utf-8"
>
>hello guys,
>Â
>is there any idea how to extract no. of connections from trejectory....................?
>
>
>
>Ravi Datta Sharma
>Lecturer,
>Bioinformatics,
>Department of Microbiology,
>CCS Unversity,
>Meerut
>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
>
>
>
> Check out the all-new face of Yahoo! India. Go to http://in.yahoo.com/
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>------------------------------
>
>Message: 4
>Date: Fri, 29 Aug 2008 08:44:31 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] g_hbond + invalid command line argument -g
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <48B79ACF.8050807 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>minnale wrote:
> >
> > Thanks Justin for your reply
> > I am interested to get file which contain how many hydrogen bonds are
> > there in my protein and the bonds present between which atoms?
> > Is there anyway to get this file
> > can you please tell me,
>
>g_hbond -h
>
> > Thanks in advance for your kind suggestion
> >
> > On Thu, 28 Aug 2008 Justin A.Lemkul wrote :
> > >
> > >
> > >minnale wrote:
> > >>
> > >>Thanks Justin for your quick reply
> > >>the g_hbond command ran succesfully and gave me .xvg file and it
> > contain 3 columns
> > >>that is like
> > >>
> > >>@ title "Hydrogen Bonds"
> > >>@ xaxis label "Time"
> > >>@ yaxis label "Number"
> > >>@TYPE xy
> > >>@ view 0.15, 0.15, 0.75, 0.85
> > >>@ legend on
> > >>@ legend box on
> > >>@ legend loctype view
> > >>@ legend 0.78, 0.8
> > >>@ legend length 2
> > >>@ s0 legend "Hydrogen bonds"
> > >>@ s1 legend "Pairs within 0.35 nm"
> > >> 0 79 674
> > >> 0.2 87 687
> > >> 0.4 80 693
> > >> 0.6 69 690
> > >> 0.8 79 691
> > >> 1 74 690
> > >> 1.2 81 700
> > >> 1.4 75 681
> > >> 1.6 83 687
> > >>
> > >>the first column is time then could please tell about 2nd and 3rd columns
> > >>Thanks in advance.
> > >
> > >Read the header of the file, specifically:
> > >
> > >@ s0 legend "Hydrogen bonds"
> > >@ s1 legend "Pairs within 0.35 nm"
> > >
> > >Gromacs always prints legends for what the data mean.
> > >
> > >-Justin
> > >
> > >>
> > >>On Thu, 28 Aug 2008 Justin A.Lemkul wrote :
> > >> >
> > >> >
> > >> >minnale wrote:
> > >> >> Hi all,
> > >> >> 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
> > >> >>g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues
> > mainchain+H atoms) -num .xvg -g .log
> > >> >>its showed
> > >> >>
> > >> >>Program g_hbond, VERSION 3.3.1
> > >> >>Source code file: statutil.c, line: 799
> > >> >>
> > >> >>Invalid command line argument:
> > >> >>-g
> > >> >>
> > >> >>Can you please tell where I have done mistake?
> > >> >>Thanks in advance for your valuable suggestions.
> > >> >>
> > >> >>
> > >> >
> > >> >The error tells you exactly what the problem is. There is no such
> > option. The -g flag appears in newer versions of Gromacs.
> > >> >
> > >> >-Justin
> > >> >
> > >> >>
> > >> >>
> > >>
> > >>------------------------------------------------------------------------
> > >> >>
> > >> >>_______________________________________________
> > >> >>gmx-users mailing list gmx-users at gromacs.org
> > >> >>http://www.gromacs.org/mailman/listinfo/gmx-users
> > >> >>Please search the archive at http://www.gromacs.org/search before
> > posting!
> > >> >>Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >> >
> > >> >-- ========================================
> > >> >
> > >> >Justin A. Lemkul
> > >> >Graduate Research Assistant
> > >> >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 at gromacs.org
> > >>http://www.gromacs.org/mailman/listinfo/gmx-users
> > >>Please search the archive at http://www.gromacs.org/search before
> > posting!
> > >>Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > >-- ========================================
> > >
> > >Justin A. Lemkul
> > >Graduate Research Assistant
> > >Department of Biochemistry
> > >Virginia Tech
> > >Blacksburg, VA
> > >jalemkul[at]vt.edu | (540) 231-9080
> > >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > >========================================
> >
> >
> >
> > Rediff Shopping
> > <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>
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>--
>David van der Spoel, Ph.D., Professor of Biology
>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
>------------------------------
>
>_______________________________________________
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>
>End of gmx-users Digest, Vol 52, Issue 118
>******************************************
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