Hello AMBER users,
I am calculating the binding free energy of a complexed protein-ligand system .
However while extracting the snapshots with the command below, it shows the following message:
$ set AMBERHOME=/usr/apps/chemistry/amber/amber11
$ $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
Use of uninitialized value $ENV{"AMBERHOME"} in concatenation (.) or string at /usr/apps/chemistry/amber/amber11/exe/mm_pbsa.pl line 22.
Can't locate mm_pbsa_global.pm in .INC (.INC contains: /src/mm_pbsa /usr/lib/perl5/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/5.10.0 /usr/lib/perl5/site_perl/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.10.0 /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl .) at /usr/apps/chemistry/amber/amber11/exe/mm_pbsa.pl line 23.
BEGIN failed--compilation aborted at /usr/apps/chemistry/amber/amber11/exe/mm_pbsa.pl line 23.
I didn't understand the message very clearly. Can anyone please let me know how to solve this issue. What commands can be used instead to set the AMBERHOME ?
Please let me know. Your suggestions in this regard is highly appreciated.
Thanks
Jagur
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Received on Thu May 19 2011 - 12:00:03 PDT
