Dear Jason,
Thanks very much for your valuable advices.
It helps a lot.
They are the residues number.
I will give it a try.
Thank you!
Best regards,
Li Zhe
________________________________________
From: Jason Swails <jason.swails.gmail.com>
Sent: Friday, 9 October, 2015 9:23 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Restraints
On Fri, Oct 9, 2015 at 9:20 AM, Wong Li Zhe <Wong.LiZhe.student.imu.edu.my>
wrote:
> Dear David,
>
> Thanks for your suggestions.
> As I am new to AMBER, does that mean that after having the residues
> restrained in the 'mdin' script & before running minimization, I should
> type 'restraintmask = 373-424, 610-1198' to confirm it?
>
You need ntr=1, restraintmask=':373-424,610-1198', and restraint_wt=5.0
(where 5.0 is the force constant in kcal/mol/A^2). This replaces the card
input at the bottom of the mdin file.
> But what applications I should utilise to view the restrained residues?
>
You can use a trajectory visualization program (like VMD or Chimera) to
confirm whether or not the atoms you are trying to restrain are moving more
than you would expect.
> Or will there be any text generated to show that it has been restrained
> successfully?
>
There should be text written to the mdout file telling you how many atoms
were restrained, but it's always good to verify expectations through
visualization.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 09 2015 - 06:30:10 PDT
