On 10/01/2012 11:15 AM, BERGY wrote:
> Hi All,
> I am runnng a binding energy calculation for my protein-peptide
> system as per the tutorial. i am using amber12 with ambertool12.
> When i try the step in
> http://ambermd.org/tutorials/advanced/tutorial3/section3.htm
> i.e:
> $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa> binding_energy.log
>
> i get the following error
> -----------------------------------
>
> Use of uninitialized value $inp in concatenation (.) or string at
> /usr/soft/amber12/src/mm_pbsa/mm_pbsa_createinput.pm line 600.
> Use of uninitialized value in numeric eq (==) at
> /usr/soft/amber12/src/mm_pbsa/mm_pbsa_createinput.pm line 627.
> Use of uninitialized value $inp in concatenation (.) or string at
> /usr/soft/amber12/src/mm_pbsa/mm_pbsa_createinput.pm line 600.
> Use of uninitialized value in numeric eq (==) at
> /usr/soft/amber12/src/mm_pbsa/mm_pbsa_createinput.pm line 627.
> Use of uninitialized value $inp in concatenation (.) or string at
> /usr/soft/amber12/src/mm_pbsa/mm_pbsa_createinput.pm line 600.
> Use of uninitialized value in numeric eq (==) at
> /usr/soft/amber12/src/mm_pbsa/mm_pbsa_createinput.pm line 627.
> /usr/soft/amber12/bin/sander -O -i pbsa_com.in -o
> pbsa_com.1.out -c ./perl_toc64_com.crd.1 -p ../../tleap/complex.top
> not successful
> For details see:
> http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
> -----------------------------------
> Most likely the error output to the file pbsa_com.1.out
> which in the end reads as follows.
> -----------------------------------
> dx0 = 0.01000, drms = 0.00010
>
> ======== Implicit Solvent Initialization ========
>
> Max Nonbonded Pairs: 483084 1976072
>
> PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 2C
> ------------------------------------
>
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>
The INP related error message is caused by the absence of the INP flag
in the input file (binding_energy.mmpbsa). This input file was generated
for an older AMBER version. Please adapt the input file according to the
example input files provided in AMBER12 under src/mm_pbsa/Examples. We
plan to update the AMBER mm_pbsa.pl tutorial in the near future.
Best regards,
Nadine
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Received on Mon Oct 01 2012 - 06:00:07 PDT
