GBIS synamics

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?

     Thanks,

                                                                                                                                                         Francesco

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:38 CST