Re: [AMBER] Apply Lennar-Jones potential between small molecules

From: Ming Tang <m21.tang.qut.edu.au>
Date: Thu, 25 Feb 2021 21:17:00 +0000

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
>
> &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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Received on Thu Feb 25 2021 - 13:30:02 PST
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