AMBER Archive (2008)

Subject: AMBER: radius of calcium ion in MM_PBSA

From: Hannes Wallnoefer (Hannes.Wallnoefer_at_uibk.ac.at)
Date: Mon Jul 28 2008 - 03:18:22 CDT

Hi Amber-users,

i simulated a calcium ion containing protein with a ligand. I used the calcium
parameters from http://www.pharmacy.manchester.ac.uk/bryce/amber. Now i want to
calculate the free enregy with the mm_pbsa perl script of amber9. The snapshots
extraction works fine, but when i want to start the energy caculation the
radius of the calcium is not found (log file error: No radius found for KA
3667 in residue CAL 235). Obviously the script does not find the radius in
the parmtop file.
Does anybody know how to include the radius in the parmtop file? Which further
information is needed?

Best regards,
Hannes

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