Dear amber users,
I am running a mm_pbsa calculation for determining the binding free energy of nucli-drug complex. When i submit the job it stops by showing the following message. Kindly suggest me what could be reason.
Missing values for MM VDW
Following is my input parameters, Here i am trying both pb and gb as given in the $AMBERHOME/src/mm_pbsa/Examples/02-Mol.stability.
Reading input parameters
Found PREFIX => qb_eg2
Found PATH => ../ex1
Found COMPLEX => 1
Found RECEPTOR => 0
Found LIGAND => 0
Found COMPT => ../comp.top
Found RECPT => XXX
Found LIGPT => XXX
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 1
Found PB => 1
Found MS => 1
Found NM => 0
Found PROC => 2
Found REFE => 0
Found INDI => 1.0
Found EXDI => 80.0
Found SCALE => 2.0
Found LINIT => 500
Found PRBRAD => 1.6
Found RADIOPT => 1
Found FOCUS => 0
Found PERFIL => 80.0
Found CHARGE => ../comp.crg
Found SIZE => ../comp.siz
Found SURFTEN => 0.005
Found SURFOFF => 0.0
Found DIELC => 1.0
Found IGB => 2
Found GBSA => 1
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found INTDIEL => 1.0
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found PROBE => 0.0
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 08 2006 - 06:07:16 PDT
