On Mon, Oct 1, 2012 at 5:15 AM, BERGY <nucleic81.gmail.com> 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
>
If you search for the error message (" PB Bomb in pb_aaradi(): No radius
assigned for atom"), you'll find numerous links on the Amber archives that
describes what is happening. The solution is to use radiopt=0 so that
radii are extracted from the topology file rather than determined inside
PBSA itself.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 01 2012 - 04:30:02 PDT
