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

From: Yong Duan <>
Date: Fri, 18 Jan 2008 22:17:35 -0800

Dear Mr. Yu:
"the errors appeared!"? Can you be a bit more specific? What error message
did you receive?
-----Original Message-----
From: [] On Behalf Of
Sent: Friday, January 18, 2008 9:28 PM
Subject: AMBER: A problem to loadup the molecular in the xleap

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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Received on Sun Jan 20 2008 - 06:07:31 PST
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