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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Received on Mon Apr 25 2005 - 18:53:00 PDT
