On Feb 17, 2012, at 10:43 PM, Danny Xu wrote:
> I'd like to let the ligand diffuse freely into the receptor binding site, thus I need to fix receptor center of mass and constrain the ligand in a 3D box with the receptor enclosed so that it does not diffuse away.
>
>
Well, as Aron asked, why do you need to freeze the receptor? If the
ligand is confined within a box*, and the box is fixed (somehow) to the
receptor, they are tethered together. Translation and rotation affect both
in a similar manner. You can postprocess to account for rotation and
translation.
*IMO, this would be easier to achieve by confining the ligand within a sphere
with a very gentle one-sided harmonic exterior wall, say 1 kcal/mol-A, and
a flat well restraint of 0 kcal/mol-A within the sphere. The ligand would
freely diffuse within the sphere unless it contacted the wall or receptor
atoms. Search the archives and carefully read the section of the manual on
restraint syntax. The center of the sphere could be, for example, the center
of mass of the atoms lining the binding site. Or maybe a key receptor atom
known to interact with the ligand.
A box would be really hard to do, I believe.
Bud Dodson
>
> ________________________________
> From: Aron Broom <broomsday.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Cc: Danny Xu <quantum_mania.yahoo.com>
> Sent: Friday, February 17, 2012 8:04 PM
> Subject: Re: [AMBER] restraints in igb simulation
>
> This feels like a communication problem, but maybe its just on my side.
> But as Jason said initially without some actual details about what you want
> to do, it's hard to recommend anything. For instance, why do you want to
> freeze the receptor in the first place?
>
> On Fri, Feb 17, 2012 at 7:03 PM, M. L. Dodson <mldodson.comcast.net> wrote:
>
>>
>> On Feb 17, 2012, at 5:44 PM, Danny Xu wrote:
>>
>>> Typo, how to constrain a ligand to move within a box in igb simulations.
>>>
>>>
>>
>> I think a box might be hard to achieve, but a sphere is easy. Search the
>> mailing list archives for "flat well restraint".
>>
>> Bud Dodson
>>
>>>
>>> ________________________________
>>> From: Danny Xu <quantum_mania.yahoo.com>
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Sent: Friday, February 17, 2012 4:39 PM
>>> Subject: Re: [AMBER] restraints in igb simulation
>>>
>>> I just wanted to constrain the receptor so that it does not move from
>> its initial position and also constrain a ligand so that it only moves with
>> a box. My question is simply how to achieve this in pmemd when igb is used?
>> Any thoughts are highly appreciated.
>>>
>>> -DX
>>>
>>>
>>>
>>> ________________________________
>>> From: Jason Swails <jason.swails.gmail.com>
>>> To: Danny Xu <quantum_mania.yahoo.com>; AMBER Mailing List <
>> amber.ambermd.org>
>>> Sent: Friday, February 17, 2012 5:52 AM
>>> Subject: Re: [AMBER] restraints in igb simulation
>>>
>>> It completely depends on what you're trying to do.
>>>
>>> Without that it's hard to give anything but the most generic (unhelpful)
>> advice.
>>>
>>> Think hard about the question you are trying to answer and what
>> simulation details would be required to probe that.
>>>
>>> HTH,
>>> Jason
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>>
>>> On Feb 17, 2012, at 1:21 AM, Danny Xu <quantum_mania.yahoo.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> In an igb simulation, what would be a good approach to:
>>>>
>>>> 1. restrain the protein to remove its rotation/translation, in another
>> word, fix its center of mass
>>>> 2. confine a ligand to move only inside a defined 3D box
>>>>
>>>> Thanks very much in advance!
>>>>
>>>> -DX
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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>>
>> --
>> M. L. Dodson
>> Business email: activesitedynamics-at-gmail-dot-com
>> Personal email: mldodson-at-comcast-dot-net
>> Gmail: mlesterdodson-at-gmail-dot-com
>> Phone: eight_three_two-five_63-386_one
>>
>>
>>
>>
>>
>>
>>
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>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Fri Feb 17 2012 - 21:30:02 PST
