normal DNA/protein complex

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3 years 7 months ago #4803 by Hegedus
DNA/protein complex was created by Hegedus
Hi,

Is it possible to perform CG simulations on DNA/protein complexes?
E.g. separate the DNA and protein into separate pdb files to be able to use different (prt/dna) martinize.py scripts then merge the topology files...

If not, what is the expected time frame for preparing martini to do this?

Thanks a lot,
Tamas

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3 years 7 months ago - 3 years 7 months ago #4807 by jaakko
Replied by jaakko on topic DNA/protein complex
Hi Tamas,

this is possible exactly the way you suggested. Separate the structures to different files, run the two martinize scripts and combine the CG structures into the same simulation box.

We're preparing a tutorial right now on how this should be done.

- Jaakko
Last edit: 3 years 7 months ago by jaakko.

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3 years 7 months ago #4810 by Hegedus
Replied by Hegedus on topic DNA/protein complex
Hi,

Thanks.
The first steps work OK: I generated separate CG DNA and CG protein and merged into one CG file.
I generated a box with water. Energy minimization was ok with the modified example.mdp

However, the short equilibration stopped pretty soon using the example.mdp

Step 60, time 0.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.313441, max 7.028124 (between atoms 202 and 200)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
201 200 90.0 0.2170 1.3620 0.2170
202 200 90.0 0.2649 2.1275 0.2650
202 201 90.1 0.3221 0.8779 0.3220

Back Off! I just backed up step60b_n0.pdb to ./#step60b_n0.pdb.1#

Back Off! I just backed up step60c_n0.pdb to ./#step60c_n0.pdb.1#
Wrote pdb files with previous and current coordinates

Step 61 Warning: pressure scaling more than 1%, mu: 1.02362 1.02362 1.02362

Step 61 Warning: pressure scaling more than 1%, mu: 1.02362 1.02362 1.02362

Step 61 Warning: pressure scaling more than 1%, mu: 1.02362 1.02362 1.02362

Step 61 Warning: pressure scaling more than 1%, mu: 1.02362 1.02362 1.02362
Segmentation fault

It seems that it may not be a simple blowing up and I can not track down the problem.
The output of energy minimizaiton contains 3705 water molecules (this is OK).
The intermediate output of the the equilibration (step60b_n0.pdb) contains only 811 waters.

Thanks for you help and hints,
Tamas

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3 years 7 months ago #4812 by jaakko
Replied by jaakko on topic DNA/protein complex
Hi,

the step*.pdb files contain particles only from a single core so the number of particles is often much lower.

Without more information I'd recommend you to run the equilibrium with a smaller time step first and see how that goes. Did you check the max force after energy minimization?

- Jaakko

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3 years 7 months ago #4824 by Hegedus
Replied by Hegedus on topic DNA/protein complex
Jaakko, Thanks.

Indead the problem starts earlier than the equilibration.

I merged the prt and dna CG models; put in a box and in water.
Energy minim as example, just integrator = steep, nsteps = 50000

The energy minimization stops/completes as:
Step= 611, Dmax= 1.6e-06 nm, Epot= -7.91436e+04 Fmax= 1.27466e+03, atom= 238
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 10 (whichmay not be possible for your system). It


However, when I check the structure, significant distortions are visible in both the DNA and protein.
Please see

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(left is before, right is after emin)

---
I noticed that grompp copmlained about bead names. Could not this cause problems with the force field (dna or protein).

Warning: atom name 1 in prt_dna.top and prt-dna-water.gro does not match (BB - BB2)
Warning: atom name 2 in prt_dna.top and prt-dna-water.gro does not match (SC1 - BB3)
Warning: atom name 3 in prt_dna.top and prt-dna-water.gro does not match (BB - SC1)
Warning: atom name 4 in prt_dna.top and prt-dna-water.gro does not match (SC1 - SC2)
Warning: atom name 5 in prt_dna.top and prt-dna-water.gro does not match (BB - SC3)
Warning: atom name 6 in prt_dna.top and prt-dna-water.gro does not match (BB - BB1)
Warning: atom name 7 in prt_dna.top and prt-dna-water.gro does not match (SC1 - BB2)

Thanks for your help and suggestion,
Tamas

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3 years 7 months ago #4830 by jaakko
Replied by jaakko on topic DNA/protein complex
Hi Tamas,

what grompp is telling you is that your .gro and .top files are in disagreement. It looks like some atoms that are defined to be part of protein in .top file are defined as DNA in the .gro file. Try checking that the order of molecules is the same in both of these files.

- Jaakko

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