[AMBER] Problem with initial complex structure for TI

From: Kalenkiewicz, Andrew (NIH/NICHD) [F] <"Kalenkiewicz,>
Date: Fri, 11 Dec 2015 23:17:11 +0000

Dear Amber users,

I'm attempting to carry out thermodynamic integration on my system using Hannes Loeffler's T4-lysozyme tutorial as a template. Everything has proceeded fine except for the van der Waals simulation with lambda = 1. In that case I get a "vlimit exceeded" error, which I know is usually due to overlapping atoms. The receptor conformation isn't ideal for the V1 state (I used the bound conformation of V0), i.e. there do look to be some possible vdw clashes. I don't really understand why it would only lead to a crash for lambda = 1 whereas the other lambdas appear fine. Any help with this would be much appreciated!


Andrew Kalenkiewicz
Postbaccalaureate Fellow, NICHD
Molecular Biology BS '13
Biomedical Engineering MSE '15
University of Michigan, Ann Arbor
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Received on Fri Dec 11 2015 - 15:30:03 PST
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