From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Jun 13 2017 - 13:37:05 CDT
Free energy calculations involving large flexible molecules are
difficult. Your best bet is to use restraints to maintain the
conformations and then do further calculations to remove the biases
introduced by the restraints as has been done for protein–protein
binding:
http://doi.org/10.1021/ct400273t
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us
On Tue, Jun 13, 2017 at 1:30 PM, Mehdi Bagherpour <mehdi.bpour_at_gmail.com> wrote:
> Dear NAMD users,
>
> I am using the ABF simulation for protein-DNA system in NAMD. Actually I
> have dimer-protein that are binding to DNA and I want to pull first monomer
> of protein vertically in order to get some idea about its binding affinity
> to DNA. My selected colvar is the distance between COM of first monomer and
> COM of its related interacted DNA. I have use distanceZ option as below:
>
> The total mass of protein monomer = 8105.1
> The total mass of related DNA = 4309.73
>
>
> colvarsTrajFrequency 1000
> colvarsRestartFrequency 1000
>
> colvar {
>
> name chADistance
>
> width 0.1 # 0.1 Angstrom of estimated fluctuation width
>
> lowerboundary 16
> upperboundary 36
>
> lowerwallconstant 200.0
> upperwallconstant 200.0
> # difference of two distances
> distanceZ {
> oneSiteSystemForce yes
>
> # e.(r-r1)
>
> axis (-13.28, -6.63, -6.3)
> # atoms of first monomer of protein
> main {
> atomNumbersRange 1-1093
> atomNumbersRange 3330-3339
> }
> # atoms of first related DNA
> ref {
> atomNumbersRange 2215-2437
> atomNumbersRange 3073-3295
> }
> }
> }
>
>
> abf {
> colvars chADistance
> fullSamples 500
> }
>
>
>
> In simulation at first protein monomer is departing a bit from DNA (around 2
> Angstrom) and then instead of protein monomer, DNA is staring to bend in
> order to be apart of protein.
>
> In fact this is not the case and I want to see the just effect of protein
> leaving DNA without any force on DNA.
>
> My question is: Do you have any idea what can I do in ABF without putting
> any external constrains on DNA in order to prevent DNA bending?
>
> Looking forward to hearing your ideas.
>
> Cheers,
> Mahdi
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