[gmx-users] Re: gmx-users Digest, Vol 52, Issue 118
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 29 11:59:37 CEST 2008
minnale wrote:
>
> 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
>
Use a newer version of Gromacs.
Or, if you suspect a certain group is involved in hydrogen bonding, create an
index group for it and pass the index file to g_hbond.
-Justin
> On Fri, 29 Aug 2008 gmx-users-request at gromacs.org wrote :
> >Send gmx-users mailing list submissions to
> > gmx-users at gromacs.org
> >
> >To subscribe or unsubscribe via the World Wide Web, visit
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> >or, via email, send a message with subject or body 'help' to
> > gmx-users-request at gromacs.org
> >
> >You can reach the person managing the list at
> > gmx-users-owner at gromacs.org
> >
> >When replying, please edit your Subject line so it is more specific
> >than "Re: Contents of gmx-users digest..."
> >
> >
> >Today's Topics:
> >
> > 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
> > >
> > >========================================
> >-------------- next part --------------
> >An HTML attachment was scrubbed...
> >URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20080829/aa271446/attachment-0001.html
> >
> >------------------------------
> >
> >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/
> >-------------- next part --------------
> >An HTML attachment was scrubbed...
> >URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20080828/31908157/attachment-0001.html
> >
> >------------------------------
> >
> >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
> >
> >
> >------------------------------
> >
> >_______________________________________________
> >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!
> >
> >End of gmx-users Digest, Vol 52, Issue 118
> >******************************************
>
>
>
> Ebay
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2401775_2394076/2397136/1?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
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list