Thank you so much Marcos!
Can you please tell me how you obtained the BOND, ANGLE and DIHEDRAL
parameters and also the NONBON for CT and HC?
Best,
Andy
On 04/07/2017 02:58 PM, Marcos Serrou do Amaral wrote:
> Hi Andy,
>
> I am sending to you ACN parameter files for this new 6-site model.
> In leap, you should use these lines:
> source leaprc.water.tip3p
> loadamberparams ACN_model.prm
> ACN = loadmol2 acn-model.mol2
>
> Please, double check all parameters.
>
> HTH,
>
>
> ---
> Marcos S.A.
>
>
> On Wed, Apr 5, 2017 at 12:08 PM, Andreas Tosstorff <
> andreas.tosstorff.cup.uni-muenchen.de> wrote:
>
>> Dear all,
>>
>>
>> thank you for your replies! As David pointed out, setting up the
>> simulation was not the problem, but it's the separation of the two
>> solvents, as seen in the attached pictures.
>>
>> After the suggested google search I came across a paper titled "New
>> Six-site Acetonitrile Model for Simulations of Liquid Acetonitrile and its
>> Aqueous Mixtures" by NIKITIN and LYUBARTSEV from 2007 (attached to this
>> mail).
>>
>> They report that they were able to succesfully simulate water-acetonitrile
>> mixtures with their acetonitrile model. They furthermore state that their
>> model can easily be included into AMBER.
>>
>> So how do I do this?
>>
>> Do I write an .frcmod and .lib file for acetonitrile using the parameters
>> (Lennard-Jones parameters, charge, what else?) they published and then
>> rebuild my system in tleap?
>>
>>
>> This is completely new to me so I would really appreciate your help!
>>
>>
>> Best,
>>
>> Andy
>>
>>
>>
>> On 04/05/2017 05:00 PM, David Cerutti wrote:
>>
>>> You will not have an extra time with this if you want your simulation to
>>> go
>>> a long time. For starters you can use the AddToBox utility in amber/bin
>>> (run with no arguments to see the list of things you can do). That will
>>> help you randomly mix acetonitrile and water initially (make sure to
>>> minimize before starting dynamics).
>>>
>>> But if you simulate just a few hundred acetonitriles and a thousand waters
>>> (or whatever the ratio needs to be), then check after 50ns or so, and find
>>> that they separate (which appears likely) you have as DAC said an
>>> imbalance
>>> in your FF and a parameter development problem.
>>>
>>> Once you get your solvents to stay mixed, round II: protein in solvent
>>> mixture. You could very well find that the protein gets coated in
>>> acetonitrile and that the acetonitrile gets leached out of solution in the
>>> process. To determine whether THAT is realistic or not you will need the
>>> right kind of experimental data.
>>>
>>> Dave
>>>
>>> On Apr 5, 2017 10:48 AM, "Sowmya Indrakumar" <soemya.kemi.dtu.dk> wrote:
>>>
>>> Hi Andreas,
>>>> I am not sure if this is feasible.
>>>> Since you already know the ratio, you can do the following
>>>> 1.solvate you protein
>>>> 2.replace some of the water with the other molecule. For instance,
>>>> *addions* randomly replaces water with the ion you give.
>>>> Regards
>>>> Sowmya
>>>> ________________________________________
>>>> From: David A Case [david.case.rutgers.edu]
>>>> Sent: Wednesday, April 05, 2017 4:37 PM
>>>> To: AMBER Mailing List
>>>> Subject: Re: [AMBER] Acetonitrile Water Mix
>>>>
>>>> On Wed, Apr 05, 2017, Andreas Tosstorff wrote:
>>>>
>>>>> I am trying to simulate a protein in a 60% acetonitrile, 40% water
>>>>>
>>>> mixture.
>>>>
>>>>> I observed that the two solvents arrange in layers rather than to form a
>>>>> homogeneous mix. See the attached pictures and input files.
>>>>> Any advice on how to perform simulations with solvent mixtures?
>>>>>
>>>> Sounds like you already know how to perform the simulations. If these
>>>> two
>>>> liquids are supposed to be miscible, then there is likely an inbalance in
>>>> your
>>>> force field. Try a Google search on something like "acetonitrile water
>>>> force
>>>> field" to see what others have done in simulating this sort of mixture.
>>>>
>>>> ....dac
>>>>
>>>>
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>>>>
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>>>>
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>>>
>> --
>> M.Sc. Andreas Tosstorff
>> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
>> Department Pharmazie
>> LMU München
>> Butenandtstr. 5-13 ( Haus B)
>> 81377 München
>> Germany
>> Tel.: +49 89 2180 77059
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Fri Apr 07 2017 - 07:00:02 PDT
