AMBER Archive (2004)

Subject: AMBER: minimization of GLH

From: Hailong Lin (hailong.lin_at_stud.man.ac.uk)
Date: Mon Apr 05 2004 - 06:57:31 CDT

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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