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
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Received on Fri Feb 17 2012 - 16:30:02 PST
