[gmx-users] gromos parameterisation in OPLS

Tue Jun 17 14:21:09 CEST 2008

On Tue, 17 Jun 2008 17:31:53 +0530 (IST)
  ANINDITA GAYEN <aninditagayen at yahoo.co.in> wrote:
> 
> 
> can i put the partial charges from Gaussian?
In principle you can do everything assuming that it is justified.

Putting charges from Gaussian do not mean much. It sounds very elaborated
because Gaussian could imply that you include "ab initio" calculations.
However Gaussian also include semi-empirical methods!

All that to say that the manner the charges are extracted from Gaussian
is much more relevant to be able to judge their quality.

What you have to do is to convince yourself that the way you do is the
accurate enough to the application you like.

In a general manner the RESP (see Amber web site) approach has shown
to be relative reliable.

> --- 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
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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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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------