normal martinize.py

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12 years 4 months ago #833 by Rajat Desikan
martinize.py was created by Rajat Desikan
Hi
I have a protein consisting of 298 residues, but when I use martinize.py, only 294 residues are displayed. What is the problem? Is there a limit on the length of residues?

Also, In the protein tutorial, I don't see any section pertaining to addition of ions. Don't we need to add ions to the solvated protein?

And I still have to manually add the disulfide bond linkages, right?

Lastly (and I am sorry for bugging you guys so much), what is the difference between seq2itp.pl, atom2cg.awk and martinize.py?

Thank you so much for your patience. :)

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12 years 4 months ago #834 by jantunes
Replied by jantunes on topic martinize.py
Hey,

You don't need to add ions in all proteins, that depends in what u want/protein you use, I think (I never used ions)

U can check differences between martinize and seq2itp here http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum/topic?id=113&p=1#p527 , but in resume seq2itp gives you topologies and atom2cg gives you CG structure (like names says) and martinize gives both.

Cumps,

Jorge

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12 years 4 months ago #835 by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py
Thanks for the quick reply :)
In the fully atomistic simulations, we add Na and Cl ions to the protein in a waterbox to neutralize charges right?...I was wondering if I needed to do that here

And secondly, When I coarse grained a protein having 298 residues, the cg structure contained on 294 residues. Even in the cg Ubq structure in the tutorial, the number of amino acids in the atomistic pdb and the cg pdb do not match. Am I missing something?

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12 years 4 months ago #836 by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py
Well, I have this protein oligomer (huge one) in water. It has total charge of -120. Should I not add ions? If so, how do I add them? Thanks...

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12 years 4 months ago #837 by djurre
Replied by djurre on topic martinize.py
If you have to add ions depends on what you want to study and there is no one who can judge that better then you. If you want to add ions though it is easy. Use genion, and make sure the ions have the same name as the ones in "martini_v2.0_ions.itp". Also don't forget to include that file in your top file.

About your other questions, where only 294 out of 298 residues are displayed, there are two reasons I can think of:
1) Four residues in the protein are not part of the main of the main chain. They could be a seperate peptide or water. Although I think martinize.py should at least give a warning about that.
2) The last residue in the protein may be 298 but the first one is maybe residue 5 instead of 1? It just gets renumbered so it seems there are less residues.

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12 years 4 months ago #838 by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py
Hi Djurre, thanks for the quick reply
No, the residue numbering for both start from -4. The FG pdb ends at residue 298 while the cg pdb ends at 294. I am totally stumped. here are the first and last few lines of the pdb file.

FG:
CRYST1 84.470 84.470 142.690 90.00 90.00 90.00 P 1 1
ATOM 1 N GLY A -4 37.685 -8.089 123.218 1.00 62.07 N
ATOM 2 CA GLY A -4 38.810 -7.596 124.066 1.00 28.32 C
ATOM 3 C GLY A -4 39.113 -6.132 123.822 1.00 50.03 C
ATOM 4 O GLY A -4 38.598 -5.423 122.944 1.00 25.53 O
ATOM 5 N ILE A -3 40.027 -5.655 124.648 1.00 31.98 N
ATOM 6 CA ILE A -3 40.504 -4.283 124.633 1.00 35.13 C
ATOM 7 C ILE A -3 41.184 -3.940 123.304 1.00 26.90 C
ATOM 8 O ILE A -3 40.946 -2.886 122.689 1.00 22.72 O
ATOM 9 CB ILE A -3 41.460 -4.096 125.832 1.00 33.48 C
ATOM 10 CG1 ILE A -3 41.796 -2.615 125.951 1.00 33.70 C
ATOM 11 CG2 ILE A -3 42.711 -4.972 125.716 1.00 25.13 C
ATOM 12 CD1 ILE A -3 40.623 -1.704 126.140 1.00 35.69 C
.............

ATOM 2328 N LYS A 294 33.906 15.700 76.165 1.00 19.46 N
ATOM 2329 CA LYS A 294 34.615 14.429 76.112 1.00 17.14 C
ATOM 2330 C LYS A 294 33.746 13.440 75.326 1.00 18.25 C
ATOM 2331 O LYS A 294 32.567 13.321 75.591 1.00 25.12 O
ATOM 2332 CB LYS A 294 34.910 13.885 77.528 1.00 18.83 C
ATOM 2333 CG LYS A 294 35.858 12.669 77.475 1.00 29.03 C
ATOM 2334 CD LYS A 294 36.276 12.274 78.865 1.00 22.49 C
ATOM 2335 CE LYS A 294 37.014 10.959 79.005 1.00 32.80 C
ATOM 2336 NZ LYS A 294 37.332 10.731 80.451 1.00 35.20 N
ATOM 2337 N LYS A 295 34.359 12.785 74.351 1.00 18.28 N
ATOM 2338 CA LYS A 295 33.565 11.860 73.528 1.00 33.87 C
ATOM 2339 C LYS A 295 33.403 10.471 74.126 1.00 30.15 C
ATOM 2340 O LYS A 295 32.307 9.901 73.992 1.00 39.25 O
ATOM 2341 CB LYS A 295 34.200 11.794 72.134 1.00 27.43 C
ATOM 2342 CG LYS A 295 34.198 13.143 71.409 1.00 49.24 C
ATOM 2343 CD LYS A 295 32.802 13.768 71.418 1.00 40.45 C

ATOM 2344 CE LYS A 295 32.818 15.233 71.024 1.00 80.00 C
ATOM 2345 NZ LYS A 295 31.671 15.974 71.630 1.00 73.80 N
ATOM 2346 N THR A 296 34.433 9.924 74.775 1.00 27.00 N
ATOM 2347 CA THR A 296 34.274 8.568 75.340 1.00 26.06 C
ATOM 2348 C THR A 296 33.821 8.601 76.788 1.00 35.96 C
ATOM 2349 O THR A 296 34.041 9.597 77.480 1.00 27.34 O
ATOM 2350 CB THR A 296 35.566 7.733 75.257 1.00 27.05 C
ATOM 2351 OG1 THR A 296 36.596 8.377 76.017 1.00 28.09 O
ATOM 2352 CG2 THR A 296 35.901 7.613 73.770 1.00 25.55 C
ATOM 2353 N LEU A 297 33.208 7.500 77.201 1.00 29.68 N
ATOM 2354 CA LEU A 297 32.699 7.458 78.592 1.00 25.77 C
ATOM 2355 C LEU A 297 33.463 6.413 79.400 1.00 34.45 C
ATOM 2356 O LEU A 297 33.556 5.221 79.118 1.00 29.77 O
ATOM 2357 CB LEU A 297 31.199 7.204 78.522 1.00 30.79 C
ATOM 2358 CG LEU A 297 30.458 7.061 79.854 1.00 79.89 C
ATOM 2359 CD1 LEU A 297 30.456 8.386 80.600 1.00 48.88 C
ATOM 2360 CD2 LEU A 297 29.053 6.530 79.593 1.00 37.48 C
ATOM 2361 N PHE A 298 34.110 6.896 80.460 1.00 28.55 N
ATOM 2362 CA PHE A 298 34.906 6.073 81.350 1.00 34.27 C
ATOM 2363 C PHE A 298 34.001 5.093 82.116 1.00 43.53 C
ATOM 2364 O PHE A 298 33.012 5.643 82.681 1.00 42.33 O
ATOM 2365 CB PHE A 298 35.712 6.974 82.295 1.00 42.55 C
ATOM 2366 CG PHE A 298 36.630 6.145 83.156 1.00 60.44 C
ATOM 2367 CD1 PHE A 298 36.204 5.626 84.370 1.00 71.35 C
ATOM 2368 CD2 PHE A 298 37.920 5.902 82.728 1.00 39.23 C
ATOM 2369 CE1 PHE A 298 37.057 4.864 85.149 1.00 55.80 C
ATOM 2370 CE2 PHE A 298 38.776 5.137 83.508 1.00 53.02 C
ATOM 2371 CZ PHE A 298 38.352 4.624 84.711 1.00 41.60 C
END


(the lines in bold are not martinized)

CG:

MODEL 1
CRYST1 84.470 84.470 142.690 90.00 90.00 90.00 P 1 1
ATOM 1 BB GLY A -4 38.523 -6.755 123.459 1.00 2.00
ATOM 2 BB ILE A -3 40.662 -4.149 123.766 1.00 2.00
ATOM 3 SC1 ILE A -3 41.648 -3.347 125.910 1.00 2.00
ATOM 4 BB LEU A -2 42.055 -4.348 120.993 1.00 2.00
ATOM 5 SC1 LEU A -2 45.007 -5.406 120.774 1.00 2.00
..........

ATOM 635 BB ARG A 291 29.807 18.853 78.661 1.00 0.00
ATOM 636 SC1 ARG A 291 28.198 20.484 80.772 1.00 0.00
ATOM 637 SC2 ARG A 291 27.330 20.059 83.611 1.00 0.00
ATOM 638 BB HIS A 292 33.052 19.432 77.737 1.00 22.00
ATOM 639 SC1 HIS A 292 33.234 20.853 79.831 1.00 22.00
ATOM 640 SC2 HIS A 292 32.128 21.757 81.808 1.00 22.00
ATOM 641 SC3 HIS A 292 32.029 22.766 80.338 1.00 22.00
ATOM 642 BB GLY A 293 33.345 17.104 75.088 1.00 0.00
ATOM 643 BB LYS A 294 33.631 14.210 75.797 1.00 0.00
ATOM 644 SC1 LYS A 294 35.681 12.943 77.956 1.00 0.00
ATOM 645 SC2 LYS A 294 37.185 10.836 79.784 1.00 0.00
TER
ENDMDL


I also checked...residues 295-298 are not a separate peptide...here is the martinize option I gave

./martinize.py -f modprotein.pdb -o protein.top -x cg_protein.pdb -ss modprotein.dssp -p backbone

Please help me out...

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12 years 4 months ago #840 by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py
Thanks to Djurre and Durba, the problem got sorted out.
The problem was in the dssp file created and then used in martinize.py using -ss option. Instead, I ran the dssp binary directly along with martinize.py.
Thanks

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