On Tue, Feb 9, 2016 at 2:10 PM, A kS <aks25121986.gmail.com> wrote:
> Respected Sir,
>
> Thank you very much for your reply.The installation logic is now quite
> clear to me. Just to make sure that I understood it properly I used an
> example of AmberTools14/15:
>
> 1. export AMBERHOME = 'pwd' : *will set the 'pwd' as AMBERHOME*
> 2. doing ./configure gnu: *will configure the application*
> 3. export amber.sh : *will *
>
This should be "source amber.sh".
> * (a) export AMBERHOME and *
> * (b) check if LD_LIBRARY_PATH (for example) is set or not, if *NOT*
> then it will set LD_LIBRARY_PATH="${AMBERHOME}/lib", *else* it
> will append the **"${AMBERHOME}/lib" to the
> LD_LIBRARY_PATH.*
> 4. make install : install the Amber
> 5. export "source $AMBERHOME/amber.sh" >> ~/.bashrc" :
> *will add* **exactly** this "source $AMBERHOME/amber.sh" line to
> .bashrc. *So if I open .bashrc I will find that line written in the
> .bashrc.* *This will ensure that when ever I login the login shell source
> the respective amber.sh file.*
>
>
> ***********************************************************************************************
> I have one more technical question and I hope you will not mind If I
> discussed :
>
> I want to install, 1. Amber12 coupled with AmberTools13, 2.AmberTools14
> and 3. AmberTools15 one by one in a system:
>
There is no point to installing both AmberTools 14 and AmberTools 15 --
they both offer exactly the same programs and are both free. The only
difference is that AmberTools 14 is no longer supported.
>
> 1. *For Amber12+AmberTools13*
>
> export AMBERHOME ='pwd'
> ./configure gnu
> make install
> the add these lines to .bashrc
> export AMBERHOME=/home/aditya/applications/amber12
> export PATH=$AMBERHOME/bin:$PATH
>
> 2. *Then for AmberTools14*
>
> *comment out following lines in .bashrc*
> #export AMBERHOME=/home/aditya/applications/amber12
> #export PATH=$AMBERHOME/bin:$PATH
> *then do:*
> export AMBERHOME='pwd'
> ./configure gnu
> source amber.sh
> make install
> echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
> This will add /home/user/ambertools14/amber.sh to .bashrc
>
> 3.*Then for AmberTools15*
>
> *Comment out following lines in .bashrc*
> #export AMBERHOME=/home/aditya/applications/amber12
> #export PATH=$AMBERHOME/bin:$PATH
> #source /home/user/ambertool14/amber.sh
> *the repeat the same as above*
>
> *Now to use only Amber12 and AmberTools13:*
>
> Changing the following lines in .bashrc
>
> export AMBERHOME=/home/aditya/applications/amber12
> export PATH=$AMBERHOME/bin:$PATH
> #source /home/user/ambertool14/amber.sh
> #source /home/user/ambertool15/amber.sh
>
> *Now to use only AmberTools14*
>
> Changing the following lines in .bashrc
>
> #export AMBERHOME=/home/aditya/applications/amber12
> #export PATH=$AMBERHOME/bin:$PATH
> source /home/user/ambertool14/amber.sh
> #source /home/user/ambertool15/amber.sh
>
This sounds about right. You can also use pmemd from Amber 12 and
AmberTools 15 by following instructions here:
http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 09 2016 - 11:30:05 PST
