[gmx-users] restraining Ca2+ ion

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 7 19:36:55 CET 2009

jayant james wrote:
> Hi!
> Thanks for your suggestions. In my protein there are two phosphorylated 
> serines (-vely charged) adjacent to each other on chain A and these 
> serines start to move towards the Ca2+ ion in chain B. It is only after 
> a while of them being close to each other that the Ca2+ starts popping 
> off. Also to modify the charges of the residues adjoining the Ca2+ 
> ion, what file should I be looking for to make these changes? would it 
> be the topology file? 

Well, that behavior may not be entirely unexpected.  Two adjacent phosphates 
would likely repel each other, making it difficult to bind ions at that 
location.  Is there some basis to suggest that Ca2+ should even bind there?

Yes, charges are in your topology.  If you generated your .top with pdb2gmx, 
then obviously there are entries in the appropriate .rtp file that can be 
modified to generate future topologies with the same charges.

> As per your suggestions I would be going with the PME so should the mdp 
> file modified to incorporate the parameters below be sufficient?!!

Well, assuming those are the appropriate cutoff's for your force field, and the 
rest of your .mdp file is satisfactory (and you actually specify PME), then it 
is probably reasonable enough.


> ns_type        =  grid
> rlist              =  1.0
> rcoulomb      =  1.0
> rvdw             =  1.4
> vdwtype        =  cut-off
> fourierspacing = 0.12
> fourier_nx      = 0
> fourier_ny      = 0
> fourier_nx      = 0
> pme_order     = 4
> ewald_rtol     =  1e-5
> optimize_fft   = yes
> disre            =  simple
> disre_weighting     =  equal
> Thanks
> Jayant James
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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