AMBER Archive (2009)

Subject: [AMBER] Error in MM PBSA

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Tue Jun 02 2009 - 08:42:16 CDT

Dear All,
I am using Amber 10..I am performing MM PBSA calculations to calculate the binding free energy of a ligand docked in a protein...
I performed Moleular docking and i am using the same pose for calculating the binding free energy...

When i am running the mm_pbsa.pl script for binding energy calulations i am getting the following error:

 molsurf: molsurf.c:1055: is_buried: Assertion
`sarg1 >= 0.0' failed.
sh: line 1: 6670 Aborted /opt/amber10/exe/molsurf
snapshot_com.pqr.23 0.0 >snapshot_com.mslog.23
molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.
sh: line 1: 7372 Aborted /opt/amber10/exe/molsurf
snapshot_rec.pqr.31 0.0 >snapshot_rec.mslog.31
    No data for 0+1 MM BOND 100

[10] Exit 26 mm_pbsa.pl
binding_energy.mmpbsa >binding_energy.log
 

how should i take care of this..

thank you

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