RE: AMBER: How to test the used parameters.

From: Ross Walker <>
Date: Wed, 11 Aug 2004 10:33:56 -0700

Dear Tarek,
I'm not sure what you meant by "LEaP did not like it to be alone in the pdb
file." If you setup a zinc atom as a residue in it's own right, with a
charge and VDW parameters then there is no reason why it needs to be bound
to anything. Please email the error message you get etc.
As for saving the pdb file and then looking at the bonds this won't tell you
anything because Leap does not use any connectivity data from pdb files.
Your visualisation program is almost certainly bonding by distance. However,
if you view things in the xleap editor then the bonds shown there will be
"real" bonds, I.e those that will be saved to the pdb file.
Your best option is to create a pdb file with just zinc in it. Load this is
leap as unit ZNA (or something similar). Edit ZNA, edit the zinc atom and
set the type to ZNA and the element to Zn and the charge to whatever you
calculated using Resp. Then save this as an xleap library file. saveoff ZNA
Next edit yourself an frcmod file and enter the mass and VDW parameters for
ZNA. Edit your pdb and change the residue name to ZNA - add TER cards around
the ZNA.
Then in leap load the xleap library file and the frcmod file. load your pdb
file and the single zinc atom containing residue should be recognised. You
can then save your prmtop file and you should get an unbound zinc atom in
All the best
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |


From: [] On Behalf Of
tarek mahfouz
Sent: 11 August 2004 09:56
Subject: AMBER: How to test the used parameters.

Hello all,
 I have a zinc ion in my pdb file that is non-covalently linked to the
protein. LEaP did not like it to be alone in the pdb file. I created a
frcmod file that had mass and R* and epsilon parameters but still LEaP
was complaining. I had to include it within a HIS residue and create a
" .in" file for the modified HIS residue. I did not want to do this
because I did not want the Zn to be bonded to any residue. LEaP read in
the pdb file this time but when I checked the unit there was missing bond
and angle parameters which I purposly did not add. Anyway, I added
those parameters and when I saved the pdb the zinc was bonded to the 2
histidines. I do not want these bonds, what shall I do? or is it ok to
leave them? Will the deletebond work in this case for further minimization
and MD?
  The other question I have is the parameters I used. I got them from a
reference, how to know they best represent! my system? what kind of
tests I need to do?


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Received on Wed Aug 11 2004 - 18:53:00 PDT
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