[gmx-users] gromos parameterisation in OPLS
Marc F. Lensink
lensink at bigre.ulb.ac.be
Tue Jun 17 14:48:55 CEST 2008
On Tue, Jun 17, 2008 at 02:21:09PM +0200, Xavier Periole wrote:
> 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.
although i would probably go for a b3lyp approach or so,
semi-empirally-derived charges are not necessarily a bad thing,
especially when a solvent reaction field was used. in any case
they're a million times better than mulliken.
> 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.
agreed.
cheers,
marc
> >--- 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
> >>>>>
> >>>> over India. Go to
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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
> >>>>
> >>>> ========================================
> >>>>
> >>>
> >>>
> >>> Connect with friends all over the world. Get
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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
> -----------------------------------------------------
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--
--
Marc F. Lensink
Centre for Structural Biology and Bioinformatics CSBB
Université Libre de Bruxelles marc.lensink at ulb.ac.be
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