On Thu, Mar 8, 2012 at 1:40 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
>
> Hello,
>
> 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?
>
Amber 11 uses 1.2 as the default SCEE value for every dihedral and it uses
2.0 as the default SCNB value for every dihedral.
Your simulation should be fine to move from Amber 10 to Amber 11.
There's no way to specify SCNB/SCEE currently in the prmtop short of adding
those sections yourself by hand with any Amber-released software at this
point.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 08 2012 - 13:00:04 PST
