AMBER Archive (2004)

Subject: AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd

From: Anna Schrey (anna_amber_at_web.de)
Date: Thu Jan 08 2004 - 04:30:37 CST

dear AMBER community,

I am trying to minimize a protein containing a - manually parametrized -
small-molecule ligand. This is my sander input file

  &cntrl
     imin=1, scee=1.2,
     ntpr=100, maxcyc=10000,
     cut=8.0,
     dielc=1,
     nsnb=25, ntr=0, drms=x,
     ntmin=0, ncyc=10, ntb=0,nmropt=y,
  &end
  &wt type='END' &end
LISTOUT= MINRUNamb51_0_nsmb100_4.violations
DISANG=fsh.rst
Positional restraints on TM domains
1
FIND
CA * * *
SEARCH
RES 1 319
END
END
STOP

I setup a followup of minimizations with different drms limits (1, 0.5,
0.1, 0.05, 0.01) and calculated with nmropt both 0 and 1 (the results
were similar). Using AMBER 5, I got down to rmsd about 0.1. Using AMBER
7, I only got down down to about 0.5, including several LINMIN FAILUREs.
Setting the nsnb value to 100 had no effect.

I would be pleased if somebody would be able to help me.

Best regards,

Anna

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