[gmx-users] gromos parameterisation in OPLS

[Justin A. Lemkul]

Parameterization should always be done according to the derivation of 
the original force field.  I don't know all the specifics of the OPLS-AA 
parameterization, so you'll have to look into it. 

-Justin

ANINDITA GAYEN wrote:
> can i put the partial charges from Gaussian?
> --- On Tue, 17/6/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>   
>> From: Justin A. Lemkul <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] gromos parameterisation in OPLS
>> To: aninditagayen at yahoo.co.in, "Gromacs Users' List" <gmx-users at gromacs.org>
>> Date: Tuesday, 17 June, 2008, 4:00 PM
>> If you include in the .itp file all the necessary
>> combinations in those 
>> sections, then yes, the .itp file is reasonable and will
>> use the OPLS-AA 
>> parameters for those specified items.  Take care to get the
>> numbering 
>> right after that point, because you will likely be
>> inserting lots of 
>> hydrogens!
>>
>> -Justin
>>
>> ANINDITA GAYEN wrote:
>>     
>>> Sir,
>>>
>>> If i insert the hydrogen atoms in the first section of
>>>       
>> the itp file, where atomnames , atomtypes , nr, cgnr are
>> displayed, wil it be wrong. Also, i was talking that, will
>> the inclusion of "ffoplsaa.itp" will serve the
>> bonded and nonbonded parameters if i supply the
>> connectivities in all the bonds, pairs, angles and dihedral
>> section by the atom numbers?
>>     
>>> Thanks for the requested answers.
>>>
>>> anindita
>>>
>>>
>>>
>>>
>>> --- On Mon, 16/6/08, Justin A. Lemkul
>>>       
>> <jalemkul at vt.edu> wrote:
>>     
>>>   
>>>       
>>>> From: Justin A. Lemkul <jalemkul at vt.edu>
>>>> Subject: Re: [gmx-users] gromos parameterisation
>>>>         
>> in OPLS
>>     
>>>> To: aninditagayen at yahoo.co.in, "Discussion
>>>>         
>> list for GROMACS users" <gmx-users at gromacs.org>
>>     
>>>> Date: Monday, 16 June, 2008, 9:29 PM
>>>> Changing the atomtypes will only work if you have
>>>>         
>> explicit
>>     
>>>> inclusion of 
>>>> all hydrogens in your PRODRG-generated topology. 
>>>>         
>> Since the
>>     
>>>> PRODRG 
>>>> server outputs a GROMOS-based .itp file, this is
>>>>         
>> unlikely
>>     
>>>> unless your 
>>>> molecule contains only polar or aromatic groups. 
>>>>         
>> If
>>     
>>>> we're still talking 
>>>> about CHAPS or cholesterol, this will not be the
>>>>         
>> case.  You
>>     
>>>> will have 
>>>> nonpolar groups that, within GROMOS, are atomtype
>>>>         
>> CH1, CH2,
>>     
>>>> etc., but 
>>>> OPLS will not have these UA representations.
>>>>
>>>> I'm not sure what you mean in the last
>>>>         
>> sentence. 
>>     
>>>> Nothing in this 
>>>> process will be automatically generated for you. 
>>>> You're building your 
>>>> topology by hand.  Inclusion of
>>>>         
>> "ffoplsaa.itp"
>>     
>>>> will tell grompp which 
>>>> parameters (bonded and nonbonded) apply to your
>>>>         
>> molecule. 
>>     
>>>> Calling 
>>>> "ffoplsaa.itp" will not tell any Gromacs
>>>>         
>> program
>>     
>>>> to automatically detect 
>>>> and generate bonds, dihedrals, etc. 
>>>>
>>>> The only way to have "automatic"
>>>>         
>> generation of
>>     
>>>> these parameters is to 
>>>> build an .rtp entry for your molecule that
>>>>         
>> contains all of
>>     
>>>> this 
>>>> information as well, and process your structure
>>>>         
>> with
>>     
>>>> pdb2gmx.  This is 
>>>> just as much work as building the topology
>>>>         
>> yourself, I
>>     
>>>> think.
>>>>
>>>> -Justin
>>>>
>>>> ANINDITA GAYEN wrote:
>>>>     
>>>>         
>>>>> Hi,
>>>>>
>>>>> I came to know from the mailing list that if i
>>>>>           
>> only
>>     
>>>>>       
>>>>>           
>>>> change the atomtype in the output itp file of
>>>>         
>> PRODRG2 and
>>     
>>>> put the charges as optimised by Gaussian; provided
>>>>         
>> i
>>     
>>>> include #include ffoplsaa.itp in the .top file of
>>>>         
>> the new
>>     
>>>> molecule and just keep the atom mumbers in
>>>>         
>> [bonds],
>>     
>>>> [pairs], [angles] and [dihedrals] as found in the
>>>>         
>> the all
>>     
>>>> atom pdb of PRODRG2, the resultant top file will
>>>>         
>> be a top
>>     
>>>> file in OPLS format. It was also stated there in
>>>>         
>> the
>>     
>>>> mailing list that for the atom numbers mentioned
>>>>         
>> the opls
>>     
>>>> staff will put the parameter values necccesary for
>>>>         
>> the
>>     
>>>> [bonds], [angles] etc.
>>>>     
>>>>         
>>>>> Is the approach right? 
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>       From Chandigarh to Chennai - find
>>>>>           
>> friends all
>>     
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>>>>         
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>>>> -- 
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Graduate Research Assistant
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>
>>>>         
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>     
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>>>>         
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>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>     
>
>
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================