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

[Ebert Maximilian]

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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