[AMBER] Not integer charge for glycoprotein

From: Tommaso Casalini <tommaso.casalini.mail.polimi.it>
Date: Thu, 24 Jul 2014 18:28:52 +0200

Dear Amber users and developers,
I would like to simulate a glycoprotein, whose structure is available in
pdb database.
In particular, there is this branched chain:

4YB - 4YB - VMB - OMA - OMA

This chain is attached to the protein through a ND2 - C1 bond with an ASN
The net charge of the chain is not equal to an integer value, but equal to
0.194; this is consistent with the charge of the ending group -ROH (-0.194)
that should be added for an isolated chain.

My question is: which is the best strategy to obtain an integer value of
the overall charge?

Thank you for your help.
Kind regards,
Tommaso Casalini
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Received on Thu Jul 24 2014 - 10:00:02 PDT
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