[AMBER] MMPBSA question

From: Eliac Brown <eliacbrown.yahoo.com>
Date: Sat, 19 Mar 2011 16:35:42 -0700 (PDT)

I have been reading on MMPBSA and different methodologies for SASA calculation.
As I am aware, MMPBSA.py reads the radii from the prmtop file, but the written radii in the prmtop file is the effective born radii, and this is different from the vdw radii which is needed in ICOSA calculation (after augmentation by 1.4 for the solvent probe). So, how it comes?
On the other hand, using mmpbsa.pl version, ICOSA reads the radii from compiled mdread file, but when I check the defined radii for chlorine in mdread, I couldn't find it, and the program didn't complain, why? in other case it complains such as in the case of zinc.
Any clarification would be appreciated.
Thanks in advance


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Received on Sat Mar 19 2011 - 17:00:02 PDT
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