I am looking to use amber to calculate the energies of different configurations of a protein-protein interaction. I am trying to use the imin=5 option of sander with maxcyc=1, but I am having an issue. The outputted energies always have a van der Waals contribution that is on the order of 10^16. I am just running a trajectory that has multiple copies of the crystal structure as a test. Also, the electrostatics calculated do not match those found by using imin=0 and the prmcrd file even though the coordinates in my trajectory are the same as those in the prmcrd file. My input file is:
Energy calculations
&cntrl
imin=5, ntb = 0, maxcyc=1,
igb = 2, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0,
nstlim = 0, dt = 0.001,
cut = 50.0
&end
END
END
On the command line I enter,
sander -O -i energy.in -o energy.out -p BarnaseBarstar.prmtop -c BarnaseBarstar.prmcrd -y BarnaseBarstar.mdcrd
Here is a snapshot of the problematic lines in the output file:
Maximum number of minimization cycles reached.
minimizing coord set # 1
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.6770E+16 2.1754E+16 1.3901E+18 O 2379
BOND = 11945445.8414 ANGLE = 430296.1667 DIHED = 9376.9433
VDWAALS = ************* EEL = -11230.6376 EGB = -10173.4925
1-4 VDW = 8619599.3277 1-4 EEL = 3580.9229 RESTRAINT = 0.0000
minimization completed, ENE= 0.16770484E+17 RMS= 0.217544E+17
What is it that I am doing wrong? Is something wrong with the imin=5 option of sander?
Thank you,
-Aaron van Dyne
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Received on Tue Aug 06 2013 - 14:00:03 PDT
