AMBER Archive (2009)

Subject: [AMBER] MM PBSA ERROR

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Fri Jun 12 2009 - 09:04:25 CDT

Dear All,

 I am using MM-PBSA (AMBER10) for binding free enrgy calculation...

i ran mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log..

which gave the error

   ¨ Grid origin corrected at level    
2     10.000   
33.500    20.500

PB Bomb in setgrd(): focusing grid too large    2

reset fillratio to a larger number 2.000

.............

then i set ¨ fillratio = 4¨

then i again ran the script then it gave me the error     ¨  No data for 0+2 MM BOND 119¨

Processing GB GBTOT

        Doing 1 GB GBSOL

        Doing 1 MM GAS

        Doing 1 GB GBSOL

        Doing 1 MM GAS

        Doing 1 GB GBSOL

        Doing 1 MM GAS

    Processing PB PBTOT

        Doing 1 PB PBSOL

        Doing 1 MM GAS

        Doing 1 PB PBSOL

        Doing 1 MM GAS

        Doing 1 PB PBSOL

        Doing 1 MM GAS

=>> Calc delta from raw data

what should i do now

thanks

Vikas Sharma (+91-9780449303)

Molecular Modeling lab.

Department of Medicinal Chemistry

National Institute of Pharmaceutical Education & Research (NIPER),

SAS Nagar, Mohali,

Punjab (INDIA)

      Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber