On Wed, Sep 5, 2012 at 9:36 AM, Subrata Paul <paul.subrata34.gmail.com>wrote:
> Dear Sir
>
> I want to simulate a protein and sucrose mixture with ff99SB for protein
> and GLYCAM for sucrose.
> I have installed AMBER10 with ambertools 1.5.
>
> For my simulation setup the procedure is.
>
> Xleap -f leaprc.ff99SB
> source leaprc.GLYCAM_06
> mix=loadpdb protein-sucrose.pdb
> saveamberparm mix mix.prmtop mix.inpcrd
>
> In the prmtop file it is taking both the scaling for GLYCAM and ff99SB
>
> %FLAG SCEE_SCALE_FACTOR
> %FORMAT(5E16.8)
> 5.96485232E-270 1.20000000E+00 1.00000000E+00 1.00000000E+00
> 5.96485232E-270
> 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 0.00000000E+00 0.00000000E+00
> %FLAG SCNB_SCALE_FACTOR
> %FORMAT(5E16.8)
> 9.22098365E-270 2.00000000E+00 1.00000000E+00 1.00000000E+00
> 9.22098365E-270
> 2.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 0.00000000E+00 0.00000000E+00
>
> is this scale value taking due to the ambertoots 1.5 ?
>
> but my sander is in amber10, Can I run with this scaling value?
>
No. Amber 10 does not do mixed scaling. You need Amber 11 or greater.
HTH,
Jason
P.S. The abnormally small values smell like uninitialized variables to me.
I'm pretty sure they're only occurring for dihedrals where 1-4s are not
calculated (impropers, multiterms, etc.) so it doesn't make a difference to
the calculation, but it's probably still worth fixing if it is not already
in AT 12.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 05 2012 - 13:00:10 PDT
