[gmx-users] gromos parameterisation in OPLS

[Justin A. Lemkul]

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? 
>>>
>>>
>>>
>>>
>>>
>>>
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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

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