Dear Sir/Madam,
I have beening following the Amber tutorial:
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four_orig/
and using XLEaP to implement the force field parameters for several
non-standard residues and to create the prmtop and inpcrd files.
The *prmtop and inpcrd* files were created successfully using:
saveamberparm test test.prmtop test.inpcrd
after adding water box; however, after adding ions using:
addions test Cl- 3
XLeaP failed to create the two files, and it gave the following error:
* For atom: .R<Cl- 2716>.A<Cl- 1> Could not find type: Cl-
For atom: .R<Cl- 2717>.A<Cl- 1> Could not find type: Cl-
For atom: .R<Cl- 2718>.A<Cl- 1> Could not find type: Cl-*
According to XLEaP-->"list", Cl- is already defined in the standard force
fieid that I'm using: $AMBERHOME/dat/leap/cmd/leaprc.ff10. Why XLEaP can
NOT find type Cl-?
Any help will be greatly appreciated.
Shirley
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Received on Tue May 31 2011 - 16:30:03 PDT
