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?
Is it possible?
--
*With Best Regards
Subrata
PhD Student
Dept of Chemistry.
IIT G
*
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Received on Wed Sep 05 2012 - 07:00:04 PDT
