AMBER Archive (2008)

Subject: AMBER: A problem to loadup the molecular in the xleap

From: ë (
Date: Fri Jan 18 2008 - 23:28:02 CST

Dear Dr Yong,
  I just did as your suggestion: change the ligand from the pdb format to the mol2 format in sybyl. Then the ligand can be loadup in antechamber. However, when I tried to loadup the ligand in the xleap completely the same as the tutorial did, I could still not loadup it. As follows:
  $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
source leaprc.gaff
loadamberprep imichange.prepin
loadamberparams imichange.frcmod
a = loadmol2 imichange.mol2
  charge a
  addions a Na+ 0
  (Above is very good)
  saveamberparm a a.prmtop a.inpcrd
  (the errors appeared! I could not save the file!)
  Can you give me some advice?
  Thanks in advance!
  Best wishes
  Rilei yu

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