Hello,
On Wed, Dec 12, 2012 at 6:19 AM, Amparo Garcia Lopez <
Amparo.GarciaLopez.unige.ch> wrote:
> Dear all,
>
> I get this error while trying to run min/equil on the pmemd module of
> Amber11
>
> Cannot match namelist object name scee
> namelist read: misplaced = sign
> Cannot match namelist object name .2
>
> By reading previous messages I have learnt that scee was removed from the
> cntrl namelist in Amber11.
>
> However, because of my inexperience, I'm not sure whether this means that
> I can simply remove scee from my script, or whether I have to replace it
> with something else.
>
Yes, just delete scee (and scnb) from your script. This variable is the
scaling factor for 1-4 electrostatic interactions. Since different force
fields may use different scaling factors (the notable example is GLYCAM,
which uses 1.0, and the rest of the AMBER force fields, which uses 1.2),
the only way to 'properly' combine molecules parametrized by both force
fields is to scale each dihedral with its own scaling factor. As a result,
SCEE and SCNB are now specified in the topology file.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Dec 12 2012 - 05:00:02 PST
