Hi,
have you checked whether the AMBERHOME environment variable is set
correctly?
The error output essentially says that the sander executable cannot be
found, the location of which is constructed from AMBERHOME.
Regards,
Anselm
> 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 - 05:30:03 PDT
