i am doing minimization of haloperoxidase in amber7. Glutamic acids were protonated by changing the residues name from GLU to GLH. The minimization failed due to linmin failure on the OE1 in one GLH at all time even though i have relaxed all the GLHs manually in LEap.
NSTEP ENERGY RMS GMAX NAME NUMBER
175 -1.1606E+05 1.2378E+01 1.0180E+02 OE1 5320
BOND = 234.2581 ANGLE = 3913.9892 DIHED = 2969.3549
VDWAALS = 1370.3095 EEL = -147001.1394 HBOND = 0.0000
1-4 VDW = 2297.6582 1-4 EEL = 20159.1636 RESTRAINT = 0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -1.1606E+05 1.2378E+01 1.0180E+02 OE1 5320
BOND = 234.2581 ANGLE = 3913.9891 DIHED = 2969.3548
VDWAALS = 1370.3086 EEL = -147001.1372 HBOND = 0.0000
1-4 VDW = 2297.6581 1-4 EEL = 20159.1629 RESTRAINT = 0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
the sander input is as below,
minimization
&cntrl
lastist=3000000,
lastrst=20000000,
imin=1,ncyc=100,
ntb=1, ntc=2,
ibelly=1,
maxcyc=50000, ntpr=25,
&end
Group one
5.0
ATOM 1 8874
END
Group two
5.0
ATOM 8880 43817
END
END
I've checked the environment around this GLH residue, there is no overlap or wierd structure. is it possible to skip over the annoying atom?
cheers
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Received on Mon Apr 05 2004 - 13:53:00 PDT
