I am trying to minimize a strecture that contains an anzyme and it's substrate. The complex was created by using Vina to dock the substrate to the enzyme. I followed the steps in the antechamber tutorial to make the inpcrd and prmtop files.
I tried the same exact protein without the docked ligand and it ran without error. The message below says I should try turning off SHAKE, but will that affact my results down the road here?
my min.in file:
min 1st time for ctz 2ps
&cntrl
imin=1,maxcyc=5000,ncyc=500,
cut=8.0,ntb=1,
ntc=2,ntf=2,
ntpr=100,
ntr=1,
/
Putting restraints on residues 1-305
500.0
RES 1 306
END
END
NSTEP ENERGY RMS GMAX NAME NUMBER
500 2.6120E+05 4.0553E+03 5.6572E+05 HD21 1590
BOND = 31311.4597 ANGLE = 30018.2823 DIHED = 2992.1159
VDWAALS = 98941.5229 EEL = -109489.5411 HBOND = 0.0000
1-4 VDW = 181774.5442 1-4 EEL = 13899.4160 RESTRAINT = 11752.4888
EAMBER = 249447.8000
.... RESTARTED DUE TO LINMIN FAILURE ...
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 5 780 1589 1590
*** Especially for minimization, try ntc=1 (no shake)
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Received on Sun Oct 14 2012 - 22:00:03 PDT
