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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Received on Wed Jan 14 2004 - 15:53:15 PST
