Hello Jason,
I started with the simple thing first.
I just picked up one carbon atom on surface (reg name=GRA, reg # 1153).
And chose C aplha from the center residue(#22) of my peptide.
And run makeDIST_RST
makeDIST_RST -upb 7col.dist -pdb 2hbs.pdb -rst RST.dist
in the 7col.dist file, I have
---------------------------------------
22 ARG CA 1153 GRA C 50.0
-----------------------------
with the max distance <50A
Do you think this is a correct way to set up the distance restraint?
Thank you.
Bongkeun Kim
Quoting Jason Swails <jason.swails.gmail.com>:
> You can use the nmropt functionality. See the description in Chapter 6 in
> the amber11 manual (the functionality is the same in amber10 as well).
>
> Good luck!
> Jason
>
> On Mon, Dec 6, 2010 at 4:40 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
>
>> Hello,
>>
>> I'm going to use the implicit solvent MD study of peptide on surface.
>> Because of absence of the periodic boundary condition, I want to give
>> a distance restraint between flat surface molecule and the peptide
>> whose maximum distance between the centers of mass will be less than
>> 20Angstrom.
>> Do you have any idea how to set this up?
>> Thank you.
>> Bongkeun Kim
>>
>>
>>
>>
>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Mon Dec 06 2010 - 15:00:02 PST
