Hi Amber users,
I calculated free energies using MMPBSA.py using a complex including
bromine. So I got the following error
Bad atom type: br
Refering to an older mailing list entry I used the make-mdins flag and
changed the gbsa from gbsa=2 to gbsa=1 an started the
calculation again which worked fine then. I already calculated the energies
of some other ligands docked to the same protein using gbsa=2 and want to
compare
those. So my questition is if they are still comparable or how big is the
difference between those options gbsa=1 and gbsa=2?If they are not is there
a faster option to
get away from this bad atom type error or do I have to calculate the other
complexes with gbsa=1 again?
Thanks in advance
Bernhard Poll
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Received on Tue Apr 05 2011 - 08:00:02 PDT
