AMBER Archive (2003)

Subject: AMBER: question about input files for small molecule with fluorine

From: aini_at_rwja.umdnj.edu
Date: Mon Nov 03 2003 - 09:45:10 CST

Dear Ambers,

    I met a wierd probelm with my small molecule with fluorine atom inside.
I used antechamber and parmchk to prepare .prep and .frcmod file for it.
The input file for protein-ligand complex were generated using xleap. when
I run my minimization with the script "min.in", a error message: bad atom
type: f and the job was stopped. Why I didn't get complain about atom type
in xleap?

The content of my min.in:
cat <<eof > mdin
  minimize structure
 &cntrl
  imin = 1, maxcyc = 1500, ncyc = 1000,
  igb = 2, saltcon = 0.002, gbsa = 1,
  cut = 500,
  ntpr = 50, ntx = 1, ntb = 0,
  ntr = 1,
 &end
  keep all atoms frozen
  250
RES 669-919
END
END
eof
sander -O -i mdin \
-c AR.crd -p AR.top -ref AR.crd \
-o AR.min.out -r AR.rst

Thank you very much!
aini

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