[AMBER] Can I use Amber 10 PRMTOP with Amber 11?

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Thu, 8 Mar 2012 13:40:32 -0500


I would like to extend an MD run for which I have a trajectory produced
by Amber 10 PMEMD. I have a PRMTOP file created for an RNA
molecule in explicit solvent with ions, using ff99SB. This file does
not contain any sections defining the SCEE parameters. In Amber 10
I was using scee=1.2 in the input file. I understand I have to remove it to
get Amber 11 to start. The latest Amber Tools manual states that the default value
is 1.2, and it must be explicitly defined for force fields older than
the 1994 revisions. Can I continue may old Amber 10 run in Amber 11
with the older PRMTOP file without the SCEE section? If, so, will the
scee = 1.2 be used by default? If not, how could I augment the old PRMTOP
file with the SCEE info?

Thank you in advance, Voytek Kasprzak

Wojciech (Voytek) Kasprzak [Contractor]
Analyst Programmer,
Basic Science Program, SAIC-Frederick, Inc.
National Cancer Institute in Frederick, Frederick, MD
(301) 846 5537
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Received on Thu Mar 08 2012 - 11:00:04 PST
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