Hi,
It seem the export went ok. Did you still get the error of "Error - must
define AMBERHOME environment variable"?
Thanks.
On Wed, Jun 8, 2011 at 3:26 PM, souvik sur <souviksur.hotmail.com> wrote:
>
> Dear sir,
> This is the following message :
>
>
>
>
> [root.nis ~]# AMBERHOME=/home/cshrc/amber9/
> [root.nis ~]# export AMBERHOME
> [root.nis ~]# env
> ORBIT_SOCKETDIR=/tmp/orbit-root
> HOSTNAME=nis.server
> IMSETTINGS_INTEGRATE_DESKTOP=yes
> SHELL=/bin/bash
> TERM=xterm
> HISTSIZE=1000
>
> XDG_SESSION_COOKIE=31fd11201947efa211d767e40000000f-1307508140.187667-1787110966
> GTK_RC_FILES=/etc/gtk/gtkrc:/root/.gtkrc-1.2-gnome2
> WINDOWID=29360132
> QTDIR=/usr/lib64/qt-3.3
> OLDPWD=/home/cshrc/amber9
> QTINC=/usr/lib64/qt-3.3/include
> IMSETTINGS_MODULE=none
> NO_PROXY=localhost,127.0.0.0/8
> USER=root
> http_proxy=http://proxy.du.ac.in:3128/
>
> LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.tbz=01;31:*.tbz2=01;31:*.bz=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01
;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
> SSH_AUTH_SOCK=/tmp/keyring-EFFnHh/socket.ssh
> GNOME_KEYRING_SOCKET=/tmp/keyring-EFFnHh/socket
> ftp_proxy=ftp://proxy.du.ac.in:3128/
> FTP_PROXY=ftp://proxy.du.ac.in:3128/
> USERNAME=root
> SESSION_MANAGER=local/unix:.
> /tmp/.ICE-unix/2202,unix/unix:/tmp/.ICE-unix/2202
> ALL_PROXY=socks://proxy.du.ac.in:3128/
> all_proxy=socks://proxy.du.ac.in:3128/
>
> PATH=/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/bin:/bin:/root/bin:/root/bin
> MAIL=/var/spool/mail/root
> DESKTOP_SESSION=gnome
> QT_IM_MODULE=xim
> PWD=/root
> XMODIFIERS=.im=none
> GDM_KEYBOARD_LAYOUT=us
> GNOME_KEYRING_PID=2193
> KDE_IS_PRELINKED=1
> LANG=en_US.UTF-8
> GDM_LANG=en_US.UTF-8
> KDEDIRS=/usr
> https_proxy=https://proxy.du.ac.in:3128/
> HTTPS_PROXY=https://proxy.du.ac.in:3128/
> GDMSESSION=gnome
> HISTCONTROL=ignoredups
> SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
> SHLVL=2
> HOME=/root
> no_proxy=localhost,127.0.0.0/8
> GNOME_DESKTOP_SESSION_ID=this-is-deprecated
> HTTP_PROXY=http://proxy.du.ac.in:3128/
> LOGNAME=root
> CVS_RSH=ssh
> QTLIB=/usr/lib64/qt-3.3/lib
>
> DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-CZWCSGcpt1,guid=ead8ed036f3d4b1b54e145fa00000036
> LESSOPEN=|/usr/bin/lesspipe.sh %s
> WINDOWPATH=1
> DISPLAY=:0.0
> AMBERHOME=/home/cshrc/amber9/
> G_BROKEN_FILENAMES=1
> COLORTERM=gnome-terminal
> XAUTHORITY=/var/run/gdm/auth-for-root-5FycYT/database
> _=/usr/bin/env
>
>
>
> regards,
> Souvik Sur
> Ph. D. Student
> Department Of Chemistry
> University Of Delhi
> India
>
>
>
>
> > Date: Wed, 8 Jun 2011 15:17:32 +0800
> > From: teonghan.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] Loadin AMBER9 in linux
> >
> > Hi,
> >
> > Can you type env and post your output here after you export AMBERHOME?
> >
> > Thanks.
> >
> > On Wed, Jun 8, 2011 at 3:10 PM, souvik sur <souviksur.hotmail.com>
> wrote:
> >
> > >
> > > Dear sir,
> > > how can I export AMBERHOME variable because in every time I export it
> but
> > > still it was not working and what can I write in home directory's
> .bashrc
> > > file for exporting amberhome environment variables?
> > >
> > > regards,
> > > Souvik Sur
> > > Ph. D. Student
> > > Department Of Chemistry
> > > University Of Delhi
> > > India
> > >
> > >
> > >
> > >
> > > > Date: Wed, 8 Jun 2011 14:47:29 +0800
> > > > From: teonghan.gmail.com
> > > > To: amber.ambermd.org
> > > > Subject: Re: [AMBER] Loadin AMBER9 in linux
> > > >
> > > > Hi,
> > > >
> > > > Most likely you did not export the AMBERHOME environment variable. Do
> > > that
> > > > by typing "export AMBERHOME=/path_to_your_amber_directory/" in
> terminal.
> > > A
> > > > more permanent way of doing this is to write that command in your
> home
> > > > directory's .bashrc file.
> > > >
> > > > Thanks.
> > > >
> > > > On Wed, Jun 8, 2011 at 2:42 PM, souvik sur <souviksur.hotmail.com>
> > > wrote:
> > > >
> > > > >
> > > > > Dear sir
> > > > > I have successfully installed AmberTools 1.5, now how can I know
> Amber
> > > is
> > > > > running rightly as the xleap and tleap command are still not
> running
> > > and
> > > > > show commands not found and show the following error after giving
> the
> > > > > command make test.serial:
> > > > >
> > > > > cd leap; ./Run.tleap
> > > > > Error - must define AMBERHOME environment variable
> > > > > make: *** [test.leap] Error 1
> > > > >
> > > > >
> > > > >
> > > > > regards,
> > > > > Souvik Sur
> > > > > Ph. D. Student
> > > > > Department Of Chemistry
> > > > > University Of Delhi
> > > > > India
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > > Date: Tue, 7 Jun 2011 09:11:36 -0600
> > > > > > From: jason.swails.gmail.com
> > > > > > To: amber.ambermd.org
> > > > > > Subject: Re: [AMBER] Loadin AMBER9 in linux
> > > > > >
> > > > > > There's no need to use tleap from amber9 when you can install
> > > AmberTools
> > > > > 1.5
> > > > > > (in which this bug is fixed) for free.
> > > > > >
> > > > > > HTH,
> > > > > > Jason
> > > > > >
> > > > > > On Tue, Jun 7, 2011 at 4:54 AM, TH Chew <teonghan.gmail.com>
> wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > I posted the same problem yesterday and Jason replied. It is
> most
> > > > > likely a
> > > > > > > bug related to 64bit OS. This morning, I manage to get it
> compile
> > > with
> > > > > test
> > > > > > > running fine on a 32bit OS. Can you post what you have in
> > > > > test/ff94_prm.out
> > > > > > > here?
> > > > > > >
> > > > > > > Thanks.
> > > > > > >
> > > > > > > On Tue, Jun 7, 2011 at 6:44 PM, souvik sur <
> souviksur.hotmail.com>
> > > > > wrote:
> > > > > > >
> > > > > > > >
> > > > > > > > Dear sir,
> > > > > > > >
> > > > > > > > Here is the following error in test of "leap"
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > [root.nis test]# make test.leap
> > > > > > > > cd leap; ./Run.tleap
> > > > > > > >
> > > > > > > > Running leap tests on ./tleap -> ../../exe/teLeap
> > > > > > > >
> > > > > > > > building force field libraries:
> > > > > > > >
> > > > > > > > '91 ff..
> > > > > > > >
> > > > > > > > diffing ../../dat/leap/lib/all_amino91.lib with
> all_amino91.lib
> > > > > > > > PASSED
> > > > > > > >
> ==============================================================
> > > > > > > > diffing ../../dat/leap/lib/all_aminoct91.lib with
> > > all_aminoct91.lib
> > > > > > > > PASSED
> > > > > > > > hello sir,
> > > > > > > >
> > > > > > > > Here is the following error :
> > > > > > > >
> > > > > > > >
> ==============================================================
> > > > > > > > diffing ../../dat/leap/lib/all_aminont91.lib with
> > > all_aminont91.lib
> > > > > > > > PASSED
> > > > > > > >
> ==============================================================
> > > > > > > > diffing ../../dat/leap/lib/all_nucleic91.lib with
> > > all_nucleic91.lib
> > > > > > > > PASSED
> > > > > > > >
> ==============================================================
> > > > > > > > diffing ../../dat/leap/lib/ions91.lib with ions91.lib
> > > > > > > > PASSED
> > > > > > > >
> ==============================================================
> > > > > > > >
> > > > > > > > '94 ff..
> > > > > > > >
> > > > > > > > diffing ../../dat/leap/lib/all_amino94.lib with
> all_amino94.lib
> > > > > > > > PASSED
> > > > > > > >
> ==============================================================
> > > > > > > > diffing ../../dat/leap/lib/all_aminoct94.lib with
> > > all_aminoct94.lib
> > > > > > > > PASSED
> > > > > > > >
> ==============================================================
> > > > > > > > diffing ../../dat/leap/lib/all_aminont94.lib with
> > > all_aminont94.lib
> > > > > > > > PASSED
> > > > > > > >
> ==============================================================
> > > > > > > > diffing ../../dat/leap/lib/all_nucleic94.lib with
> > > all_nucleic94.lib
> > > > > > > > PASSED
> > > > > > > >
> ==============================================================
> > > > > > > > diffing ../../dat/leap/lib/ions94.lib with ions94.lib
> > > > > > > > PASSED
> > > > > > > >
> ==============================================================
> > > > > > > >
> > > > > > > > loadpdb and saveamberparm: 94 ff..
> > > > > > > >
> > > > > > > > ./Run.tleap: Program error in leap
> > > > > > > > make: *** [test.leap] Error 1
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > regards,
> > > > > > > > Souvik Sur
> > > > > > > > Ph. D. Student
> > > > > > > > Department Of Chemistry
> > > > > > > > University Of Delhi
> > > > > > > > India
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > > Date: Tue, 7 Jun 2011 18:11:23 +0800
> > > > > > > > > From: teonghan.gmail.com
> > > > > > > > > To: amber.ambermd.org
> > > > > > > > > Subject: Re: [AMBER] Loadin AMBER9 in linux
> > > > > > > > >
> > > > > > > > > Hi Souvik,
> > > > > > > > >
> > > > > > > > > I actually come across this yesterday. Did you compile in a
> > > 64bit
> > > > > Linux
> > > > > > > > OS?
> > > > > > > > >
> > > > > > > > > Thanks.
> > > > > > > > >
> > > > > > > > > On Tue, Jun 7, 2011 at 6:08 PM, souvik sur <
> > > souviksur.hotmail.com>
> > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > sir,
> > > > > > > > > >
> > > > > > > > > > Just now i have installed amber9 in linux but when i run
> make
> > > > > > > > > > "test.serial",there showed an error in loading "leap":
> > > > > > > > > > loadpdb and saveamberparm: 94 ff..
> > > > > > > > > >
> > > > > > > > > > ./Run.tleap: Program error in leap
> > > > > > > > > > make: *** [test.leap] Error 1
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > what can I do for it?
> > > > > > > > > >
> > > > > > > > > > regards,
> > > > > > > > > > Souvik Sur
> > > > > > > > > > Ph. D. Student
> > > > > > > > > > Department Of Chemistry
> > > > > > > > > > University Of Delhi
> > > > > > > > > > India
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > _______________________________________________
> > > > > > > > > > AMBER mailing list
> > > > > > > > > > AMBER.ambermd.org
> > > > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > Regards,
> > > > > > > > > THChew
> > > > > > > > > _______________________________________________
> > > > > > > > > AMBER mailing list
> > > > > > > > > AMBER.ambermd.org
> > > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
> > > > > > > > AMBER.ambermd.org
> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > Regards,
> > > > > > > THChew
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Jason M. Swails
> > > > > > Quantum Theory Project,
> > > > > > University of Florida
> > > > > > Ph.D. Candidate
> > > > > > 352-392-4032
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Regards,
> > > > THChew
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Regards,
> > THChew
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
THChew
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 08 2011 - 01:00:02 PDT
