NAMD cal with AMBER forces: Polarizable parameters in AMBER

From: Xiao Ju Zhang (xiaojuzh_at_gmail.com)
Date: Thu Dec 16 2010 - 13:21:01 CST

Dear all,

Does anyone happen to use AMBER forcefields in NAMD? Does NAMD give same
initial energy (bond, angel, and dihedral ect.), as it use the same input
generated by AMBER and AMBER forcefields?

I am trying to simulate RNA molecule with NAMD using the initial inputs
generated from AMBER, and the forcefield for the simulation is AMBER
forcefield 99. In the user guide, there is a chapter clearly instructs how
to do it. In the Caveat section, the guidance mentions that " Polarizable
parameters in AMBER are not supported. " What I am not sure is, does this
mean that even with the same input and AMBER ff99 parameters, the starting
energy is somehow different than it should be in AMBER?

Any comment or suggest will be very welcome.

Thank you in advance, and happy holidays!

Ju

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