Respected Sir,
Thank you very much for your reply and valuable suggestions. This clear my
doubts and of course I will use AmberTools15 instead of AmberTools14.
Thank you very much once again.
Regards
On Wed, Feb 10, 2016 at 12:48 AM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> 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
>
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Received on Tue Feb 09 2016 - 22:00:04 PST
