AMBER Archive (2009)

Subject: [AMBER] polarizable force field for 18-crown-6

From: Gert von Helden (helden_at_fhi-berlin.mpg.de)
Date: Thu Apr 16 2009 - 12:33:15 CDT

Hi,
I am running some calculations on a gas-phase peptide - 18-crown-6
complex. I generate structures via REMD and then optimize selected
structures via DFT (BP86). Using the ff99SB force field, the peptide
backbone does not seem to be right. There is a section which might
(should) be beta-sheet like. When I run the REMD calculations and
impose contraints to give be beta sheet structures, the final DFT
structures are lower in energy, compared to those obtained from
unconstrained REMD (which are nowhere close to beta sheet like).
Might using a polarizable force field (such as amoeba or ff02) give me
"better" results? If so, did anybody generate polarizable force field
parameters for 18-crown-6? Is it involved to do so? Also, could one
mix force fields to describe the peptidic part using a polarizable
force field and the 18-crown-6 part using a standard force field?

Thanks in advance,
Gert

-------------------------------------
Gert von Helden, Ph.D.
Fritz-Haber-Institut der Max-Planck-Gesellschaft
Faradayweg 4-6
14195 Berlin
Germany
tel.: +49-30-8413 5615
fax: +49-30-8413 5603

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber