AMBER Archive (2005)

Subject: AMBER: radius parameter for F atom

From: Ye MEI (ymei_at_itcc.nju.edu.cn)
Date: Mon Apr 25 2005 - 12:05:06 CDT

Dear Amber Users,

I am trying mm_pbsa to calculate the binding free energy of a ligand containing F atoms to a peptide. I set PROC=2, so pbsa in amber8 is used to analysis the trajectory, instead of delphi. I guess amber should read charge and radius parameters from prmtop file. But the pbsa failed with an error message as following:
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA
        Generate PQR
        No radius found for F1 15606 in residue EFZ 946
I am sure the prmtop file contains the radii parameters for all the atoms including F atoms. So I cannot think out why this error is encountered. Will anyone oblige me with the solution to this failure?

Ye MEI
ymei_at_itcc.nju.edu.cn
2005-04-26

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