Hello all
I am running a tutorial (AMBER ADVANCED TUTORIALS TUTORIAL 3MM-PBSA -
Section 3.1 : Calculate the binding free energy of a protein-protein complex
(Ras-Raf).)
For this I am using perl script :- mm_pbsa.pl provided with amber10.
When I am calculating the binding energy it is giving following error:
Use of uninitialized value in concatenation (.) or string at
/home/sangita/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line 191.
Can't exec "-O": No such file or directory at
/home/sangita/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line 197.
-O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p
./ras-raf.prmtop not successful
I haved checked mm_pbsa_calceneent.pm at position 191 there is -O not defined
but -i,
-o, -c -p defined:
my $command = $r_pro->{"SANDER"} . " -O" .
" -i " . $nsan .
" -o " . $sanout .
" -c " . $ncrdfile .
" -p " . $npar;
What I should do for binding energy calculation.Can anybody suggest me any
solution.
sangita kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Fri Aug 13 2010 - 05:00:03 PDT
