[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 :
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>  >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
>  > >
>  > >========================================
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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,
>>  >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
>  > >  >
>  > >  >========================================
>  > >
>  > >
>  > >
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>  >--
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>  >Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>  >Box 596, 75124 Uppsala, Sweden. Phone:     +46184714205. Fax: +4618511755.
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>  >End of gmx-users Digest, Vol 52, Issue 118
>  >******************************************
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-- 
========================================

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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