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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Received on Mon Oct 01 2012 - 02:30:04 PDT
