Dear David, Hector and AMBER users,
eventually it worked with addIons when MG instead of Mg2+ was used
and the number of residues added was specified.
Many thanks,
Nick
On Thu, Feb 08, 2018, Nikolay N. Kuzmich wrote:
>
> 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.
Can you say exactly where the statement (that only monovalent ions can be
added) appears? That will help us improve the documentation.
...thx...dac
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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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>
> AddIons command didn't work here.
The two likely problems:
a. You didn't source a leaprc.water.xxx file, and hence did not get
divalent ions loaded. You can check this using the "list" command
tleap to see if you have (say) a unit called MG.
b. You made some mistake in calling addions.
If looking closely at the tleap output doesn't pinpoint the problem, please
provide the complete tleap commands and the associated error message.
....dac
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Received on Thu Feb 15 2018 - 07:00:02 PST
