GBIS synamics

From: Francesco Oteri (
Date: Wed Mar 02 2011 - 05:02:29 CST

Dear NAMD users,
I'd run a Generalized Born Implicit Solvent MD with AMBER force-field.
I've two question related to the method:

1) In the AMBER user manual where this method is described, it is cited
a Solvent Accessible Surface dependent term, but I don't find any
related term in the NAMD user guide. How is treated this term?

2) In the AMBER manual, the authors say:

/With this option, you should use the LEaP command "set default PBradii
mbondi2" or "set default PBradii bondi" to prepare the prmtop file
     Is It true for NAMD?



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