AMBER Archive (2006)

Subject: AMBER: Missing values for MM VDW

From: bala (bala_at_igib.res.in)
Date: Thu Oct 05 2006 - 06:33:14 CDT

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

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