Maybe you want to use the latest AmberTools release for your calculations,
which is better supported on the mailing list.
Ray
On Fri, Nov 9, 2012 at 1:18 AM, baogen duan <dbaogen.gmail.com> wrote:
> 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 - 10:00:02 PST
