[AMBER] Order of ff99SB and GLYCAM when using xleap

From: Sai Kumar Ramadugu <sramadugu.gmail.com>
Date: Thu, 8 Dec 2011 11:07:19 -0600

Dear Amber Users,
I have a complex of protein with a disaccharide. When I load the ff99Sb
first and GLYCAM second versus GLYCAM first and ff99SB second, the energy
terms for a zero step minimization in gas phase are different for angle,
dihedral, 1-4LJ, 1-4Coulomb, and the total potential energy.
Below are the output values from the respective minimizations:
 1. ff99SB first, GLYCAM second

      1 -1.3061E+03 1.3969E+02 3.4776E+03 SG 1025

 BOND = 85.4389 ANGLE = 175.7590 DIHED =
 VDWAALS = 855.0251 EEL = -7406.8357 HBOND =
 1-4 VDW = 428.9510 1-4 EEL = 4324.2069 RESTRAINT =

2. GLYCAM first and ff99SB second

      1 -2.3382E+02 1.3969E+02 3.4776E+03 SG 1025

 BOND = 85.4389 ANGLE = 170.9682 DIHED =
 VDWAALS = 855.0251 EEL = -7406.8357 HBOND =
 1-4 VDW = 430.1394 1-4 EEL = 4750.1157 RESTRAINT =

The differences appear due to the different values of equilibrium angle
value and force constant value for one atom,
the dihedral angle force constants and phase are different, the scee and
scnb values are different after the mixed scaling is included. Therefore
the respective energy terms are different in the output files.

Is it due to the fact that some of the atomtypes are same in both ff99SB
and GLYCAM and the parameters get overwritten based on the order of
inclusion of leaprc files in xleap?
When I was going through the manual (AmberTools) for carbohydrates, the
order in the manual is load GLYCAM first and ff99SB second.
Does this mean that whenever you have a protein and sugar complexed, the
order of leaprc files is always 1st GLYCAM and 2nd ff99SB?

Any suggestions will be helpful.

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Received on Thu Dec 08 2011 - 09:30:02 PST
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