[gmx-users] OPLS/AA parameters for 2-propanol

[Vitaly V. Chaban]

It is difficult to get a very wrong density, especially for relatively
rigid compounds. In the meantime, deviations of density within 2% of
the experimental value should be admitted acceptable.

A better criterion is to compare self-diffusion or viscosity to the
experiment. Another famous property for parametrization is heat of
vaporization.






On Wed, Sep 2, 2015 at 3:22 PM, Ebert Maximilian <m.ebert at umontreal.ca> wrote:
> Thanks for the reply. I think I found relatively good atom types for iso propanol and derived the partial charges using antechamber and red server. I next check the density of pure iso propanol and used the closest definition to the real value. Iso propanol is used as co-solvent with water with a water:iso propanol ration of 90:10. I will just use my derived parameters then.
>
> Thanks for your replies.
>
> Max
>
>> On Sep 2, 2015, at 2:08 PM, Vitaly V. Chaban <vvchaban at gmail.com> wrote:
>>
>> Normally, this sort of things is done via mechanical combining of the
>> known groups --  CH3, -CH, OH -- from the force field.
>>
>> If your goal is to increase accuracy for pure 2-propanol per se, then
>> play with the distribution of electronic density between OH and CH.
>>
>> If 2-propanol is to be used as a solvent for somwthing else, this does
>> ultimately not pay off.
>>
>>
>>
>>
>>
>>
>>
>>
>>> On Wed, Sep 2, 2015 at 11:42 AM, Ebert Maximilian <m.ebert at umontreal.ca> wrote:
>>> I saw the papers you mentioned but one is a not clear how they parameterized, one is missing the supporting material and the last is not showing the parameters they used. I will check with the initial paper of Jorgensen again but if I recall it correctly he mentioned some problems with iso-propanol.
>>>
>>> strange that such a common organic solvent is not easily accessible for OPLS.
>>>
>>> thanks for your help johnny!
>>>
>>> Max
>>>
>>>> On Sep 1, 2015, at 11:41 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>>>>
>>>> that was by google. I haven't parametrized forcefields.
>>>> did they just put the pieces in
>>>> http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work
>>>> for 2-propanol?
>>>>
>>>>
>>>>> On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>>>>>
>>>>> Not sure if those are for 2-propanol as a liquid or interaction between
>>>>> 2-propanol and protein.
>>>>> from googling "2 propanol opls/aa"
>>>>>
>>>>> 1. Development and Testing of the OPLS All-Atom Force Field on
>>>>> Conformational Energetics and Properties of Organic Liquids
>>>>>     The parameters are in the supporting info.
>>>>>     Seems not exactly 2-propanol. But it has parameter for organic
>>>>> liquids.
>>>>>     "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols"
>>>>>     http://pubs.acs.org/doi/abs/10.1021/ja9621760
>>>>>
>>>>> 2. A statistical model of hydrogen bond networks in liquid alcohols
>>>>>
>>>>> http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf
>>>>>
>>>>> 3. Parameterization of OPLS–AA Force Field for the Conformational Analysis
>>>>> of Macrocyclic Polyketides
>>>>>     https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf
>>>>>
>>>>> On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian <m.ebert at umontreal.ca>
>>>>> wrote:
>>>>>
>>>>>> Dear list,
>>>>>>
>>>>>> I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA
>>>>>> format. Before deriving my own I thought it would be best to ask first. I
>>>>>> saw some posts that people used 2-propanol in OPLS but couldn’t find any
>>>>>> reference in google scholar.
>>>>>>
>>>>>> Thank you very much,
>>>>>>
>>>>>> Max
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