Dear Jason M. Swails
Thank for you mail.
I could not find SCEE_SCALE_FACTOR entry in my topology file.
So, it appears that I should have used Amber Tools to build it, using sleap
only was not enough.
I will .check the manual and try it.
Toshi Yui
> On Thu, May 3, 2007 at 2:18 PM, Toshifumi Yui
> <tyui.cc.miyazaki-u.ac.jp>wrote:
>
>> Dear
>>
>> My system is the complex of protein and carbohydrate molecules, which are
>> not covalently connected.
>>
>> I wish to implement a job with different SCEE and SCNB values in pmemd of
>> amber11, if possible (Unit value for carbohydrate and the default ones
>> for
>> protein.)
>> .
>> Here is my sleap input file.
>>
>> >sleap -s -f
>> >set default write14scle on
>>
>
> scale, not scle
>
>
>> >source leaprc.ff99SB
>> >source leaprc.GLYCAM_06
>>
>> >model = loadPdb comp.pdb
>> >saveamberParm model comp.parm7 comp.inp
>> >quit
>> ~
>>
>> Unfortunately, it seems not to work appropriately, and probably the
>> default
>> scaling factors have been only assigned to all of the parameters.
>>
>
> I don't know what you mean by this. It's successful if you see
> "SCEE_SCALE_FACTOR" in your topology file (and "SCNB_SCALE_FACTOR"). Note
> you have to have AmberTools 1.4 or greater for this feature (and amber11
> or
> greater to take advantage of it).
>
> HTH,
> Jason
>
>
>> I wonder if I am wrong in this regards.
>>
>> Thank you.
>>
>> Toshi Yui
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 03 2011 - 19:00:02 PDT
