From: Francesco Oteri (francesco.oteri_at_gmail.com)
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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