Issues with equilibration phase (Protein-RNA-complex)

[vas2201]

Hello,
I am running MD simulation on Protein-DNA-RNA complex. However, The DNA and RNA are dissociated in first step of the Equilibration phase. Could you please advise on this matter ?.

Attached jupyter notebook and pdb as google drive
https://drive.google.com/file/d/18_0bsrF1YEvO1XITmELEsTMFIsn92icK/view?usp=sharing

Regards
Vas

[stefdoerr]

Hi, can you show me the ACEMD input file in the equilibration folder?

[vas2201]

Thanks for your reply.

input file

---

barostat on
barostatpressure 1.01325
boxsize 117.9540023803711 148.80099487304688 127.14400482177734
coordinates structure.pdb
cutoff 9
minimize 500
parameters parameters
pme on
restart on
slowperiod 1
structure structure.psf
switchdistance 7.5
switching on
temperature 298
thermostat on
thermostatdamping 1
thermostattemperature 298
timestep 4
trajectoryfile output.xtc
trajectoryperiod 25000
atomRestraint "protein and name CA" axes xyz width "0" setpoints 1@0 0@20ns
atomRestraint "protein and noh and not name CA" axes xyz width "0" setpoints 0.1@0 0@20ns
atomRestraint "nucleic and backbone" axes xyz width "0" setpoints 1@0 0@20ns
atomRestraint "nucleic and not backbone and noh" axes xyz width "0" setpoints 0.1@0 0@20ns
run 125000

[stefdoerr]

This looks ok, it should be applying restraints on the RNA and protein so they cannot move in the first step. Are you sure it's not just a wrapping issue? Can you send a screenshot of the first simulation step where you saw them disassociated?

[vas2201]

HI,
I attached screenshot, I see frame as DNA & RNA is not complex with protein. I can't be very sure it is wrapping issue.
https://drive.google.com/file/d/1LmDsahUvFM2XYbgjNNdpxuDrhqbMWrfS/view?usp=share_link
Regards
Vas

[stefdoerr]

can you show the waters as well? Then we will know if it's a wrapping issue

[vas2201]

attached :
https://drive.google.com/file/d/1eA2Kt2AD0sU1hS3L0FvH65_7fybaNJnT/view?usp=share_link

[stefdoerr]

Yes this looks like a visualization issue due to the wrapping.
Try loading the trajectory into moleculekit and re-wrapping:

from moleculekit.molecule import Molecule
mol = Molecule("./structure.prmtop")
mol.read("output.xtc")
mol.wrap("protein or nucleic") # The geometric center of this selection will be the new wrapping center
mol.view()

[stefdoerr]

https://software.acellera.com/htmd/tutorials/WrappingTutorial.html
Here is a tutorial which explains periodic wrapping in case you find it useful

[vas2201]

Thank you.

[anicoli]

Dear @stefdoerr ,

I have a question regarding the trajectory simulation of a receptor embedded within a POPC membrane, along with water and ions, using ACEMD.

During the simulation, we followed our standard procedure of wrapping the trajectory. However, we have recently observed an issue with the wrapping of the POPC head groups. I have attached an image:

Here the usual code for wrapping:

from moleculekit.molecule import Molecule
topology = input.psf
trj_file = trj.dcd


traj = Molecule(topology)
traj.read(trj_file)

sele='protein and name CA'
traj.wrap(sele)

#output file
traj.write(trj_wrap.dcd)

Could you kindly review the code we typically use for wrapping? It seems that is not able to handling the POPC head groups, is there any difference with wrapping function from previous HTMD version?

Thank you in advance for your assistance. I look forward to your guidance on resolving this issue.

Regards,
Alessandro

[stefdoerr]

Without having the files to check I can only assume that the PSF is wrong. Either different atom order from your dcd or wrong bonds specified.