normal Palmitic acid (C16) chain MARTINI parameters

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10 years 6 months ago #1908 by nareshthota
Hi All,

I have a molecule containing C16 chain and the carboxylic acid at one termini. How to get the martini coarse grained structure for this file. My PDB looks like something like this

ATOM 1 C01 LEU E 9 5.052 -0.295 -1.321 0.00 0.00 E C
ATOM 2 C02 LEU E 9 6.223 0.681 -1.541 0.00 0.00 E C
ATOM 3 C03 LEU E 9 7.318 -0.012 -2.373 0.00 0.00 E C
ATOM 4 C04 LEU E 9 8.406 -0.562 -1.433 0.00 0.00 E C
ATOM 5 C05 LEU E 9 9.603 0.407 -1.413 0.00 0.00 E C
ATOM 6 C06 LEU E 9 10.698 -0.112 -2.365 0.00 0.00 E C
ATOM 7 C07 LEU E 9 11.779 -0.846 -1.550 0.00 0.00 E C
ATOM 8 C08 LEU E 9 12.973 0.098 -1.315 0.00 0.00 E C
ATOM 9 C09 LEU E 9 14.081 -0.213 -2.339 0.00 0.00 E C
ATOM 10 C10 LEU E 9 15.153 -1.101 -1.680 0.00 0.00 E C
ATOM 11 C11 LEU E 9 16.342 -0.227 -1.239 0.00 0.00 E C
ATOM 12 C12 LEU E 9 17.463 -0.319 -2.290 0.00 0.00 E C
ATOM 13 C13 LEU E 9 18.529 -1.325 -1.816 0.00 0.00 E C
ATOM 14 C14 LEU E 9 19.710 -0.563 -1.187 0.00 0.00 E C
ATOM 15 C15 LEU E 9 20.846 -0.435 -2.219 0.00 0.00 E C
ATOM 16 C16 LEU E 9 21.907 -1.519 -1.949 0.00 0.00 E C
ATOM 17 O02 LEU E 9 21.573 -2.639 -1.644 0.00 0.00 E O
ATOM 18 H01 LEU E 9 4.267 -0.051 -1.975 0.00 0.00 E H
ATOM 19 H02 LEU E 9 5.374 -1.276 -1.511 0.00 0.00 E H
ATOM 20 H06 LEU E 9 6.619 0.968 -0.612 0.00 0.00 E H
ATOM 21 H08 LEU E 9 8.723 -1.502 -1.775 0.00 0.00 E H
ATOM 22 H09 LEU E 9 7.746 0.682 -3.036 0.00 0.00 E H
ATOM 23 H13 LEU E 9 11.132 0.697 -2.873 0.00 0.00 E H
ATOM 24 H14 LEU E 9 9.989 0.468 -0.438 0.00 0.00 E H
ATOM 25 H17 LEU E 9 13.345 -0.043 -0.344 0.00 0.00 E H
ATOM 26 H18 LEU E 9 12.102 -1.693 -2.080 0.00 0.00 E H
ATOM 27 H21 LEU E 9 15.485 -1.820 -2.370 0.00 0.00 E H
ATOM 28 H22 LEU E 9 14.521 0.684 -2.662 0.00 0.00 E H
ATOM 29 H26 LEU E 9 16.702 -0.567 -0.313 0.00 0.00 E H
ATOM 30 H28 LEU E 9 17.906 0.625 -2.415 0.00 0.00 E H
ATOM 31 H30 LEU E 9 20.058 -1.088 -0.347 0.00 0.00 E H
ATOM 32 H31 LEU E 9 18.871 -1.885 -2.636 0.00 0.00 E H
ATOM 33 H35 LEU E 9 21.287 0.514 -2.138 0.00 0.00 E H
ATOM 34 H03 LEU E 9 4.717 -0.222 -0.329 0.00 0.00 E H
ATOM 35 H07 LEU E 9 5.880 1.531 -2.053 0.00 0.00 E H
ATOM 36 H10 LEU E 9 6.895 -0.803 -2.919 0.00 0.00 E H
ATOM 37 H11 LEU E 9 8.016 -0.655 -0.462 0.00 0.00 E H
ATOM 38 H15 LEU E 9 9.290 1.358 -1.727 0.00 0.00 E H
ATOM 39 H16 LEU E 9 10.273 -0.776 -3.059 0.00 0.00 E H
ATOM 40 H19 LEU E 9 11.381 -1.142 -0.625 0.00 0.00 E H
ATOM 41 H20 LEU E 9 12.660 1.094 -1.430 0.00 0.00 E H
ATOM 42 H23 LEU E 9 13.667 -0.717 -3.162 0.00 0.00 E H
ATOM 43 H24 LEU E 9 14.743 -1.582 -0.842 0.00 0.00 E H
ATOM 44 H27 LEU E 9 16.029 0.771 -1.148 0.00 0.00 E H
ATOM 45 H29 LEU E 9 17.061 -0.641 -3.205 0.00 0.00 E H
ATOM 46 H32 LEU E 9 18.109 -1.970 -1.102 0.00 0.00 E H
ATOM 47 H33 LEU E 9 19.393 0.395 -0.895 0.00 0.00 E H
ATOM 48 H36 LEU E 9 20.456 -0.560 -3.186 0.00 0.00 E H

I am unable to convert this using martinize script since the residue name is LEU which was produced by some software. So which name should be there to convert this using martinize script??

Thanks,
Naresh

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10 years 6 months ago - 10 years 6 months ago #1918 by Clement
Replied by Clement on topic Palmitic acid (C16) chain MARTINI parameters
Description says: Martinize is a python script to generate Martini protein topology and structure files based on an atomistic structure file.

As you pointed out, your compound is not a protein; you need to find another way to convert it to CG. Check around in the Forum and this part of the FAQ. Good luck!
Last edit: 10 years 6 months ago by Clement.

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