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
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