Dear Christina and the AMBER users!
Christina, thank you for the answer,
but this section gives only the parameters needed.
But how is it possible to add divalent ions to the system technically?
AddIons command didn't work here.
I guess it's possible to add them manually somehow
but are there any automated procedures available?
Thank you in advance,
Nick
Message: 14
Date: Thu, 8 Feb 2018 09:42:41 -0500
From: Christina Bergonzo <cbergonzo.gmail.com>
Subject: Re: [AMBER] Adding divalent ions in LEaP
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAMLwDJ0tg3beCUnGnOpSK+XcLjs9_5-shtBDz5o_Pnotxyom6w.mail.gmail.com>
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Hi,
It is possible to add divalent ions using tleap.
Page 50 of the Amber 17 manual includes section 3.6, "Ions" which specifies
the parameters available.
Divalent ions are loaded for the specific water model used (specified in
leaprc.water.????), and the default parameters are reported in:
Li, P.; Roberts, B.P.; Chakravorty, D.K.; Merz, K.M. Jr. Rational Design
of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal
Cations in Explicit Solvent. J. Chem. Theory Comput., 2013, 9, 2733?2748. 20
-Christina
On Thu, Feb 8, 2018 at 9:19 AM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
> Dear AMBER users and developers,
>
> how is it possible to neutralize/add the divalent ions to the system?
> In the manual it is stated that only monovalent ions can be added.
>
> Kind regards,
> Nick
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Received on Fri Feb 09 2018 - 03:30:02 PST
