AMBER Archive (2007)

Subject: AMBER: MM_PBSA No radius found for Br!!

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Mon Aug 13 2007 - 04:52:34 CDT

Dear, all
 
How to set radius of Br in MMPBSA calculation. there is a Br atom in my ligand.
Could someone tell me where in which file i should add the line "Br 1.50" ?
my MMPBSA calculation gave me following info(i am using Amber9)

 Calculating energy / entropy contributions
    Calc contrib for ./L3_com.crd.1
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA
        Generate PQR
        No radius found for Br 4788 in residue LAC 301
Died at /prog/AMBER9_x86_64/src/mm_pbsa/mm_pbsa_calceneent.pm line 498, <PDB> line 4790.

Thank you for any help
 
Best regards
Urszula Uciechowska
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