AMBER Archive (2005)

Subject: Re: AMBER: radius parameter for F atom

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Tue May 10 2005 - 14:49:21 CDT

Your error is not with the amber. As the error following PQR suggest,
the problems lies your parameters for molsurf. mm_pbsa does not
provide the fluorine radius parameter for molsurf so you will need to
hand edit the code yourself to enter the value.

On 4/25/05, Ye MEI <ymei_at_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_at_itcc.nju.edu.cn
> 2005-04-26
>
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