[gmx-users] pulling of a metal

[Justin A. Lemkul]

Jon Mujika wrote:
> Dear all,
> 
> I am trying to pull a metal out of the protein binding pocket following 
> a cavity in the protein structure. I followed the tutorial, but I find 
> few problems:
> 
> 1) When the metal leaves the binding pocket, some ligands "follow" the 
> metal, even that  I restrained the position of protein atoms (force 
> constant of 1000 or 3000). I would like to keep the protein as it is.
> 

Use stronger restraints and/or freezegrps.

> 2) The metal does not leave the protein through the cavity. How can I 
> define this? I can take a water molecule in the cavity as reference, but 
> I do not how to deal with this.
> 

Pull along a defined vector, i.e. pull_vec1.  You can use a water molecule that 
is initially in the desired cavity to easily calculate this vector.

-Justin

> This is the pull section in the mdp file:
> 
> pull            = umbrella
> pull_geometry   = distance
> pull_dim        = N N Y
> pull_start      = yes           ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Protein
> pull_group1     = Metal
> pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 3000          ; kJ mol^-1 nm^-2
> 
> Thanks in advance for your help
> 
> Jon Mujika
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================