[gmx-users] gromos parameterisation in OPLS

[ANINDITA GAYEN]

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? 
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
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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
> 
> ========================================


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