Dear Ye:
I think you can try "RADIOPT=0".
A value of 0 uses the cavity radii from the prmtop file. A value of 1 sets
up optimized cavity radii at the pbsa initialization phase.
On Tue, 26 Apr 2005 01:05:06 +0800, Ye MEI <ymei.itcc.nju.edu.cn> wrote:
> 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.itcc.nju.edu.cn
> 2005-04-26
>
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--
JunJun Liu
College of Chemistry
Central China Normal University
WuHan 430079
P.R. China
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Received on Tue Apr 26 2005 - 02:53:00 PDT
