AMBER Archive (2009)

Subject: Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint?

From: liu junjun (ljjlp03_at_gmail.com)
Date: Mon Feb 02 2009 - 10:25:41 CST

Dear Dr. Case and Dr. Simmerling,

I misunderstood the flatwell potential on the part beyond r1 or r4.
Thanks a lot for pointing out!

All the best!

Junjun

On Sun, Feb 1, 2009 at 1:35 PM, David A. Case <case_at_biomaps.rutgers.edu> wrote:
> On Sun, Feb 01, 2009, liu junjun wrote:
>
>> ======= NMR distance restraint file ====
>> &rst IRESID=0, iat=8385,8384, r3=3.04,
>> r4=3.1, r1=3.04, r2=3.04, rk2=8000, rk3=8000,/
>> &end
>
> When r1=r2, there is no restraint at all for distances less than 3.04
> Ang. Also, since r3 is so close to r4, there is only a very weak
> restraint on distance greater than 3.04 Ang.
>
> You should actually plot out the restraint energy as a function of
> distance to see what is happening. Based on what you wrote, you
> probably want r1 to be quite small, and r4 to be quite big.
>
> ....dac
>
>
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