Dear Shomesankar Bhunia,
Please, do not write directly to me but send your queries in the Amber
or q4md-fft mailing lists
(
http://lists.q4md-forcefieldtools.org/wws/info/q4md-fft):
if your find in your /etc/passwd:
[...]
administrator:x:1000:1000:Administrator,,,:/home/administrator:/bin/tcsh
[...]
you should get "/bin/tcsh" when you execute "echo $SHELL" in your
administrator account:
if not - logout from your login and re-login
- you might have to install tcsh
see
http://www.cyberciti.biz/faq/howto-install-csh-shell-on-linux/
yum install tcsh (for redhat)
apt-get install tcsh (for ubuntu)
regards, Francois
Quoting shomesankar bhunia <rightclickatrighttime.gmail.com>:
> *Here is my passwd file*
>
> root:x:0:0:root:/root:/bin/bash
> daemon:x:1:1:daemon:/usr/sbin:/bin/sh
> bin:x:2:2:bin:/bin:/bin/sh
> sys:x:3:3:sys:/dev:/bin/sh
> sync:x:4:65534:sync:/bin:/bin/sync
> games:x:5:60:games:/usr/games:/bin/sh
> man:x:6:12:man:/var/cache/man:/bin/sh
> lp:x:7:7:lp:/var/spool/lpd:/bin/sh
> mail:x:8:8:mail:/var/mail:/bin/sh
> news:x:9:9:news:/var/spool/news:/bin/sh
> uucp:x:10:10:uucp:/var/spool/uucp:/bin/sh
> proxy:x:13:13:proxy:/bin:/bin/sh
> www-data:x:33:33:www-data:/var/www:/bin/sh
> backup:x:34:34:backup:/var/backups:/bin/sh
> list:x:38:38:Mailing List Manager:/var/list:/bin/sh
> irc:x:39:39:ircd:/var/run/ircd:/bin/sh
> gnats:x:41:41:Gnats Bug-Reporting System (admin):/var/lib/gnats:/bin/sh
> nobody:x:65534:65534:nobody:/nonexistent:/bin/sh
> libuuid:x:100:101::/var/lib/libuuid:/bin/sh
> syslog:x:101:103::/home/syslog:/bin/false
> messagebus:x:102:105::/var/run/dbus:/bin/false
> avahi-autoipd:x:103:108:Avahi autoip
> daemon,,,:/var/lib/avahi-autoipd:/bin/false
> avahi:x:104:109:Avahi mDNS daemon,,,:/var/run/avahi-daemon:/bin/false
> couchdb:x:105:113:CouchDB Administrator,,,:/var/lib/couchdb:/bin/bash
> usbmux:x:106:46:usbmux daemon,,,:/home/usbmux:/bin/false
> speech-dispatcher:x:107:29:Speech
> Dispatcher,,,:/var/run/speech-dispatcher:/bin/sh
> kernoops:x:108:65534:Kernel Oops Tracking Daemon,,,:/:/bin/false
> pulse:x:109:114:PulseAudio daemon,,,:/var/run/pulse:/bin/false
> rtkit:x:110:117:RealtimeKit,,,:/proc:/bin/false
> saned:x:111:118::/home/saned:/bin/false
> hplip:x:112:7:HPLIP system user,,,:/var/run/hplip:/bin/false
> gdm:x:113:120:Gnome Display Manager:/var/lib/gdm:/bin/false
> administrator:x:1000:1000:Administrator,,,:/home/administrator:/bin/tcsh
>
> I highlighted the last line
>
>
>
> On Tue, Sep 4, 2012 at 3:31 AM, shomesankar bhunia <
> rightclickatrighttime.gmail.com> wrote:
>
>> Dear Francois,
>> i got the following
>>
>> administrator.ubuntu:~$ echo $SHELL
>> /bin/bash
>> administrator.ubuntu:~$ echo $PATH
>> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
>> administrator.ubuntu:~$ more $HOME/.cshrc
>> /home/administrator/.cshrc: No such file or directory
>> administrator.ubuntu:~$
>>
>> So what is the inference? thanks in advance.
>>
>> On Tue, Sep 4, 2012 at 2:11 AM, shomesankar bhunia <
>> rightclickatrighttime.gmail.com> wrote:
>>
>>> Thanks...for the help...but let me try first... i will contact you after
>>> that.. i think iam not disturbing you... i am puzzled and somehow i have to
>>> the job...thanks for the kind support once again.Take care
>>>
>>>
>>> On Tue, Sep 4, 2012 at 1:56 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>>>
>>>> Dear Shomesankar Bhunian,
>>>>
>>>> - For installing the R.E.D. tools under linux:
>>>> See
>>>> http://q4md-forcefieldtools.**org/RED/RED-II.pdf<http://q4md-forcefieldtools.org/RED/RED-II.pdf>
>>>>
>>>> - To change the shell of your account see 'chsh' at:
>>>> http://linux.die.net/man/1/**chsh <http://linux.die.net/man/1/chsh>
>>>>
>>>> or edit /etc/passwd using vi, gedit...
>>>> You search a line that starts by your login such as:
>>>> fyd:x:500:500:fyd:/home/fyd:/**bin/tcsh
>>>> ^^^^
>>>> to be modified: bash -> tcsh
>>>>
>>>> - then you logout and re-login in your account
>>>>
>>>> - then you do: echo $SHELL
>>>>
>>>> echo $PATH
>>>>
>>>> - more $HOME/.cshrc
>>>>
>>>> what do you get?
>>>>
>>>> regards, Francois
>>>>
>>>>
>>>>
>>>> I have gone through the manuals provided at the sites mentioned by you
>>>>> "
>>>>> http://q4md-forcefieldtools.**org/RED/documentation.php<http://q4md-forcefieldtools.org/RED/documentation.php>"
>>>>> but only examples
>>>>> are provided in these tutorials. Please help me out in setting the path
>>>>> .
>>>>> You have mentioned about a *.cshrc file but how to create this cshrc
>>>>> file
>>>>> and what should be its location. I am creating a .cshrc file with
>>>>> set path = ($path /usr/local/resp-2.2 /usr/local/gamess)
>>>>> and i am placing it in the working directory. I am working on a csh
>>>>> shell
>>>>> and before that i am running the cshrc file in the terminal by
>>>>> ./filename.cshrc. But that is not helping me out.Please help.
>>>>>
>>>>> a very good documentation has been provided for Mac OS at
>>>>> http://q4md-forcefieldtools.**org/RED/RED-III.x-Mac.pdf<http://q4md-forcefieldtools.org/RED/RED-III.x-Mac.pdf>but for linux to
>>>>> the
>>>>> best of my knowledge, there is no such tutorial to configure RED.Thanks
>>>>> in
>>>>> advance.
>>>>>
>>>>> On Sat, Sep 1, 2012 at 1:16 AM, FyD <fyd.q4md-forcefieldtools.org>
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>>
>>>>>> > problem again,i have my gamess installed in
>>>>>> > home/administrator not in usr /local so when i am setting path
>>>>>> through
>>>>>> > home/administrator i am getting the same problem. when i am trying to
>>>>>> > install it in usr/local permission is denied. can u help me out plz.
>>>>>> i
>>>>>> will
>>>>>> > be thankful if u plz tell me how to update LD_LIBRARY_PATH to find
>>>>>> > required library. hope u help me. thanks in advance.
>>>>>>
>>>>>> installing in /usr/local is general and allows sharing the
>>>>>> installation among users.
>>>>>>
>>>>>> you can also install gamess in your home directory; update the .cshrc
>>>>>> file accordingly if you use csh/tcsh or the .bashrc file if you use
>>>>>> bash.
>>>>>>
>>>>>> regards, Francois
>>>>>>
>>>>>> PS
>>>>>> a google search of LD_LIBRARY_PATH leads to:
>>>>>> http://tldp.org/HOWTO/Program-**Library-HOWTO/shared-**libraries.html<http://tldp.org/HOWTO/Program-Library-HOWTO/shared-libraries.html>
>>>>>>
>>>>>> http://www.wiredrevolution.**com/system-administration/how-**
>>>>>> to-correctly-use-ld_library_**path<http://www.wiredrevolution.com/system-administration/how-to-correctly-use-ld_library_path>
>>>>>>
>>>>>>
>>>>>> > On Fri, Aug 31, 2012 at 11:43 AM, shomesankar bhunia <
>>>>>> > rightclickatrighttime.gmail.**com <rightclickatrighttime.gmail.com>>
>>>>>> wrote:
>>>>>> >
>>>>>> >> Thank you very much for the support. Now i have to do my job.have a
>>>>>> nice
>>>>>> >> time.
>>>>>> >>
>>>>>> >>
>>>>>> >> On Fri, Aug 31, 2012 at 2:06 AM, FyD <fyd.q4md-forcefieldtools.org>
>>>>>> wrote:
>>>>>> >>
>>>>>> >>> Dear Shomesankar Bhunia,
>>>>>> >>>
>>>>>> >>> See
>>>>>> http://q4md-forcefieldtools.**org/RED/documentation.php<http://q4md-forcefieldtools.org/RED/documentation.php>
>>>>>> >>> Manuals available for R.E.D. III.x:
>>>>>> >>> - Using the R.E.D.-III.3 tools
>>>>>> >>> - Using the R.E.D.-III.4 tools
>>>>>> >>> - Using the R.E.D.-III.5 tools & history file
>>>>>> >>> - Using R.E.D.-III.x on Mac OS
>>>>>> >>> - Using R.E.D.-III.x on Windows OS
>>>>>> >>>
>>>>>> >>> Below are examples of .cshrc file for csh/tcsh.
>>>>>> >>> to be updated using: cd && source .cshrc
>>>>>> >>>
>>>>>> >>> RESP, Gaussian, GAMESS and Firefly programs are installed in
>>>>>> /usr/local
>>>>>> >>>
>>>>>> >>> -------- resp + gaussian 09 ----------
>>>>>> >>> # QM scratch
>>>>>> >>> setenv GAUSS_SCRDIR /tmp
>>>>>> >>> setenv g09root /usr/local
>>>>>> >>> source $g09root/g09/bsd/g09.login
>>>>>> >>> # using the standalone RESP version at
>>>>>> >>>
>>>>>> http://q4md-forcefieldtools.**org/RED/resp/<http://q4md-forcefieldtools.org/RED/resp/>
>>>>>> >>> set path = ($path /usr/local/resp-2.2)
>>>>>> >>> # using the RESP version from AmberTools
>>>>>> >>> # set path = ($path $AMBERHOME/bin)
>>>>>> >>> ------------------------------**--------
>>>>>> >>>
>>>>>> >>> -------- resp + gamess --------------
>>>>>> >>> # you might update LD_LIBRARY_PATH to find required libraries
>>>>>> >>> # GAMESS_SCRDIR is defined in the /usr/local/gamess/rungms script
>>>>>> >>> set path = ($path /usr/local/resp-2.2 /usr/local/gamess)
>>>>>> >>> ------------------------------**--------
>>>>>> >>>
>>>>>> >>> -------- resp + firefly/pc-gamess ----
>>>>>> >>> # you might update LD_LIBRARY_PATH to find required libraries
>>>>>> >>> setenv PCGAMESS_SCRDIR /tmp
>>>>>> >>> set path = ($path /usr/local/resp-2.2 /usr/local/firefly
>>>>>> >>> /user/local/openmpi32/bin)
>>>>>> >>> ------------------------------**--------
>>>>>> >>>
>>>>>> >>> regards, Francois
>>>>>> >>>
>>>>>> >>>
>>>>>> >>> > Thanks again, but i am not getting anything when i type "which
>>>>>> resp".
>>>>>> >>> Can
>>>>>> >>> > you please hint me what necessary things i have to do so that i
>>>>>> can
>>>>>> >>> > interface GAMESS and RESP with REDIII.5, that will be very
>>>>>> helpful.
>>>>>> >>> >
>>>>>> >>> > On Fri, Aug 31, 2012 at 12:51 AM, Jason Swails <
>>>>>> jason.swails.gmail.com
>>>>>> >>> >wrote:
>>>>>> >>> >
>>>>>> >>> >> Because AMBERHOME/bin may not be in your PATH. Do you find the
>>>>>> command
>>>>>> >>> >> when you type "which resp"?
>>>>>> >>> >>
>>>>>> >>> >>
>>>>>> >>> >> On Thu, Aug 30, 2012 at 3:04 PM, shomesankar bhunia <
>>>>>> >>> >>
>>>>>> rightclickatrighttime.gmail.**com<rightclickatrighttime.gmail.com>>
>>>>>> wrote:
>>>>>> >>> >>
>>>>>> >>> >> > Thanks jason for your help.As gaussian is not free, i will try
>>>>>> >>> >> GAMESS,but i
>>>>>> >>> >> > have already installed amber tools in my system than why it is
>>>>>> >>> displaying
>>>>>> >>> >> > RESP not found? Thanks in advance.
>>>>>> >>> >> >
>>>>>> >>> >> > On Thu, Aug 30, 2012 at 2:55 PM, Jason Swails <
>>>>>> >>> jason.swails.gmail.com
>>>>>> >>> >> > >wrote:
>>>>>> >>> >> >
>>>>>> >>> >> > > On Thu, Aug 30, 2012 at 2:49 PM, shomesankar bhunia <
>>>>>> >>> >> > >
>>>>>> rightclickatrighttime.gmail.**com<rightclickatrighttime.gmail.com>>
>>>>>> wrote:
>>>>>> >>> >> > > >
>>>>>> >>> >> > > > * Software checking *
>>>>>> >>> >> > > > Gaussian [ NOT FOUND ]
>>>>>> >>> >> > > >
>>>>>> >>> >> > >
>>>>>> >>> >> > > You need to install Gaussian, or use one of the alternative
>>>>>> >>> programs.
>>>>>> >>> >> > >
>>>>>> >>> >> > >
>>>>>> >>> >> > > > resp [ NOT FOUND ]
>>>>>> >>> >> > > >
>>>>>> >>> >> > >
>>>>>> >>> >> > > You also need to install resp (which you can do by
>>>>>> installing
>>>>>> >>> >> > AmberTools).
>>>>>> >>> >> > >
>>>>>> >>> >> > > The error messages in this case point out what the problem
>>>>>> is,
>>>>>> so
>>>>>> >>> don't
>>>>>> >>> >> > be
>>>>>> >>> >> > > afraid to try stuff out.
>>>>>> >>> >> > >
>>>>>> >>> >> > > HTH,
>>>>>> >>> >> > > Jason
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Received on Tue Sep 04 2012 - 03:00:03 PDT
