Hi Carlos,
Thanks. using a script to generate the input is a great idea.
I was dreaming to define a new atom type for the dummy atom defined as the centre of mass of a ligand and then define non-bonded potential between the dummy atom only😀
Thanks,
Ming
-----Original Message-----
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Friday, 26 February 2021 7:32 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
I don't think you can define the group using a residue number.
perhaps writing a script to generate the input is the best approach here.
the restraints can be read from a file.
On Thu, Feb 25, 2021 at 4:17 PM Ming Tang <m21.tang.qut.edu.au> wrote:
> Hi Carlos,
>
> Thank you very much for your guidance. I used harmonic potential
> between two group of atoms before, but it was only used for certain
> two groups of atoms. Here, I may have hundreds of small molecules, it
> will be lots of work and when the system changes, the atom id changes
> so I need to modify the igrn again. Is it doable to define dummy
> particles as the centre of mass of the ligand and apply potential to the defined dummy particles only?
>
> Thanks a lot,
> Ming
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, 26 February 2021 3:15 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Apply Lennar-Jones potential between small
> molecules
>
> sorry I meant use rk3=0, as in the example below.
>
> On Thu, Feb 25, 2021 at 12:01 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > you might try using a distance restraint that has rk2=0, this will
> > give
> no
> > penalty for distances longer than r2 and a harmonic penalty below
> > r2. You can define groups of atoms for COM distance restraints.
> >
> > check the manual for details (use the nmropt=1 option), and then
> > create a restraint that looks something like this (making sure to
> > edit the atom numbers, distances and force constants). igr1 and igr2
> > list the atoms in each COM group. r1/r2/r3/r4 define the distance
> > points where the function changes. rk2 and rk3 are the force
> > constants. The function is described
> in
> > this tutorial:
> https://urldefense.com/v3/__http://ambermd.org/tutorials/advanced/tuto
> rial4/__;!!NVzLfOphnbDXSw!XdeYXiiaomSQqpxH3W3DYLlnfegxQ85JHYSEs2DBaJRu
> qSFeZkltt8e86ZePsiwRbnt9$
> >
> > &wt
> > type='END',
> > &end
> > &rst
> > iat=-1,-1,
> > igr1=1070,1130,
> > igr2=1310,1325,1377,
> > r1=1.0, r2=10.0, r3=900.0, r4=1000.0, rk2=10., rk3=0.0, &end
> > &rst
> > iat=0,
> > &end
> >
> > On Wed, Feb 24, 2021 at 5:52 PM Ming Tang <m21.tang.qut.edu.au> wrote:
> >
> >> Dear list,
> >>
> >>
> >> I have a system of protein with lot so small molecules solvated in
> >> a water box. I want to apply force/potential between the centre of
> >> mass a group of atoms in different small molecules to prevent them
> >> from aggregation. I only know AMBER can define non-bounded
> >> interactions
> between
> >> two atoms using LJEDIT in *.frcmod. Is there a way to define a
> >> virtual particle as the centre of mass of a certain group of atoms?
> >> Does anybody have any advice for me?
> >>
> >>
> >>
> >> Thanks,
> >>
> >> Ming
> >>
> >> _______________________________________________
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> >>
> >
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Received on Thu Feb 25 2021 - 14:30:02 PST
