AMBER Archive (2004)

Subject: AMBER: "No radius found for F" error and vdw radii for F in MMPBSA

From: Ming Lei (MILei_at_clarku.edu)
Date: Tue Apr 20 2004 - 10:47:40 CDT

Hi, All:

I am running MMPBSA calculation, I get the following error message:

____________________________________________
    Calc contrib for ../01g_snapshots/B1_com.crd.1
        Calc MM/GB/SAS
        Generate PDB
        Calc PB
            Run 0
        Generate PQR
        No radius found for 28 AFL F2
_____________________________________________

Acturally, the ligand includes several fluorine atoms. I added F
information in atmtypenumbers and my_parse_delphi.siz files.
It doesnot work.

1. How do you folks handle system with ligand with F atoms using
MMPBSA?
2. What value are you using as vdw radii for F atom?

Thanks.
Ming

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