[gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Mark Abraham]

Hi,

I'd start by looking in the documentation. Section 5.3.2 of the manual
clearly suggests putting it in the ffnonbonded.itp file, which is where you
expected to find it at the start of this thread, right? :-)

Mark

On Thu, Jun 22, 2017 at 3:47 PM gozde ergin <gozdeeergin at gmail.com> wrote:

> Hey Justin,
>
> I figured out how they calculated the sigma values.
> Basically they just take the geometric mean of nitrogen and oxygen sigma
> and epsilon from ffnonbed.itp file in OPLS-AA force field
> and calculated the pairwise LJ for N-O interaction.
>
> Now I also try to add this information in my topol.top file.
> In order to do that as you have mentioned I added a section ,
>
> [ nonbond_params ]
> ; i     j       func    sigma   epsilon
> opls_287  opls_272  1  0.323161248385416  0.790543521382599
>
>
> after [ atoms ] section however I am facing with an error :
>
> Fatal error:
> Syntax error - File topol.top, line 42
> Last line read:
> '[ nonbond_params ]'
> Invalid order for directive nonbond_params
>
> Any suggestion would be appreciated.
>
> > On 21 Jun 2017, at 16:46, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> >
> > On 6/21/17 10:39 AM, gozde ergin wrote:
> >> Hi MArk,
> >> Thanks for the respond. I understood that point however I still do not
> get which sigma to change.
> >> I the paper JCTC 2017, Miller et. al. they have mentioned that they
> increase the for nitrogen–carboxylate oxygen interactions in OPLSAA.
> >> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
> notrogen and one for carboxylate oxygen.
> >>
>        sigma            epsilon
> >>  opls_287   N3   7  14.00670    -0.300       A    3.25000e-01
> 7.11280e-01
> >>  opls_272   O2   8  15.99940    -0.800       A    2.96000e-01
> 8.78640e-01
> >> Which one defines the amino nitrogen–carboxylate oxygen interactions?
> >> Which sigma should I change?
> >
> > What people are doing more and more is introducing pair-specific
> parameters to override the combination rule values.  That's likely what is
> being referred to. OPLS-AA by default does not use pair-specific LJ
> interactions, hence why you find no [nonbond_params] in ffnonbonded.itp.
> The same is true of AMBER.  CHARMM uses some (also called NBFIX in the
> literature), while GROMOS uses a ton of these.
> >
> > To override the LJ combination rules, add a [nonbond_params] directive
> with the published parameters, which refer to an *interaction*, not an atom
> type.
> >
> > -Justin
> >
> >> Thanks
> >>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >>>
> >>> Hi,
> >>>
> >>> Different force fields work differently and thus are implemented
> >>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
> sigma
> >>> is a property of the atomtype
> >>>
> >>> Mark
> >>>
> >>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeergin at gmail.com>
> wrote:
> >>>
> >>>> Dear users,
> >>>>
> >>>> I am trying to change the sigma value of amino nitrogen–carboxylate
> oxygen
> >>>> interactions in OPLSAA in GROMACS.
> >>>> However I have difficulties to understand which parameter i should
> change
> >>>> in ffnonbonded.itp file?
> >>>> I am looking something like [ nonbond_params ] section however it is
> not
> >>>> exist in ffnonbonded.itp?
> >>>> Any help would be appreciated.
> >>>>
> >>>> Thanks in advance.
> >>>> --
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> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu <mailto:
> jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul <
> http://mackerell.umaryland.edu/~jalemkul>
> >
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