Dear Nick,
Check if you have included the command "source leaprc.water.tip3p" in your
tleap or xleap, to load counterions parameters.-
greetings,
Hector.
> 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>
> Content-Type: text/plain; charset="UTF-8"
>
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
--------------------------------------
Dr. Hector A. Baldoni
Profesor Adjunto (FQByF-UNSL)
Investigador Adjunto (IMASL-CONICET)
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
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Received on Fri Feb 09 2018 - 04:30:02 PST
