Begin forwarded message:
> From: "M. L. Dodson" <mldodson.comcast.net>
> Subject: Re: [AMBER] restraints in igb simulation
> Date: February 17, 2012 11:23:20 PM CST
> To: Danny Xu <quantum_mania.yahoo.com>, AMBER Mailing List <amber.ambermd.org>
>
>
> 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
Of course the restraint units should be kcal/mol-A^2. Sorry.
>
>>
>> ________________________________
>> 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
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> --
>>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> 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
>
>
>
>
>
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 17 2012 - 21:30:03 PST
