AMBER Archive (2008)

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

From: ë (yulaomao1983_at_yahoo.com.cn)
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
   

       
---------------------------------
Ż䴫ףԺؿ
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu