Dear all,
I want to calculate the binding free energy between RNA
polymerase and Mg2ATP using mm_pbsa.pl. The snapshots for complex, receptor
and ligand were generated. But error is occurred in the course of
calculation. The error message in the log file is as follow
*Calculating energy / entropy contributions
Calc contrib for ./snapshot_com.crd.1
Checking atom numbers
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
No radius found for Mg+ 14946 in residue Mg+ 917*
**
I can not understand this because the corresponding *.prmtop files were
provided. And the VDW radius is in the top file. How to solve this
problem? Would you like to help me with this? Thanks!
Best wishes
Yours sincerely
Duan Baogen
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Received on Fri Nov 09 2012 - 01:30:02 PST
