Minimize protein-covalent ligand complex with AMBER
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This is for ligands that modify a specific residue.
(1) Make a directory:
mkdir coval_min cd coval_min/
(2) Download pdb file from the web:
wget https://files.rcsb.org/view/5YY1.pdb
(3) Manually create 3 files using your favorate text editor:
a covalent ligand, lig.pdb:
keep the sidechain of the mofifed cystien:
cat 94F_bkup.pdb
ATOM 89 CA CYS A 12 29.215 -1.013 17.747 1.00 23.10 C ATOM 92 CB CYS A 12 30.264 -1.172 18.849 1.00 23.68 C ATOM 93 SG CYS A 12 29.632 -1.020 20.503 1.00 25.01 S ATOM 1385 C31 94F A 203 16.511 -4.125 24.817 1.00 32.17 C ATOM 1386 C30 94F A 203 15.606 -4.260 23.787 1.00 32.36 C ATOM 1387 C32 94F A 203 17.840 -3.910 24.531 1.00 31.54 C ATOM 1388 C29 94F A 203 16.037 -4.183 22.484 1.00 32.47 C ATOM 1389 C19 94F A 203 21.614 -2.199 22.881 1.00 29.12 C ATOM 1390 C5 94F A 203 23.964 -5.464 22.540 1.00 29.57 C ATOM 1391 C18 94F A 203 22.453 -3.293 22.771 1.00 29.13 C ATOM 1392 C23 94F A 203 18.284 -3.829 23.223 1.00 31.43 C ATOM 1393 C22 94F A 203 19.692 -3.612 23.019 1.00 29.79 C ATOM 1394 C24 94F A 203 17.372 -3.972 22.203 1.00 32.05 C ATOM 1395 C3 94F A 203 21.900 -4.565 22.770 1.00 29.39 C ATOM 1396 C2 94F A 203 20.533 -4.693 22.895 1.00 29.45 C ATOM 1397 C20 94F A 203 20.247 -2.347 23.012 1.00 29.51 C ATOM 1398 C7 94F A 203 23.836 -3.189 22.644 1.00 28.94 C ATOM 1399 C14 94F A 203 29.536 0.583 20.690 1.00 25.47 C ATOM 1400 C13 94F A 203 28.376 1.143 21.474 1.00 26.40 C ATOM 1401 C12 94F A 203 27.093 0.850 20.795 1.00 26.10 C ATOM 1402 C9 94F A 203 23.979 -0.953 21.731 1.00 28.62 C ATOM 1403 C17 94F A 203 25.969 -2.149 22.595 1.00 29.17 C ATOM 1404 C10 94F A 203 25.024 -0.390 20.794 1.00 28.12 C ATOM 1405 C16 94F A 203 26.678 -0.809 22.586 1.00 28.22 C ATOM 1406 C25 94F A 203 17.826 -3.897 20.794 1.00 32.91 C ATOM 1407 N4 94F A 203 22.652 -5.665 22.653 1.00 29.29 N ATOM 1408 N6 94F A 203 24.595 -4.289 22.534 1.00 29.70 N ATOM 1409 N8 94F A 203 24.523 -1.948 22.642 1.00 29.33 N ATOM 1410 N11 94F A 203 26.238 0.005 21.476 1.00 27.18 N ATOM 1411 O15 94F A 203 26.847 1.362 19.713 1.00 25.34 O ATOM 1412 F1 94F A 203 19.995 -5.935 22.878 1.00 29.69 F ATOM 1413 F26 94F A 203 16.791 -3.770 19.931 1.00 34.77 F ATOM 1414 F27 94F A 203 18.674 -2.862 20.538 1.00 31.92 F ATOM 1415 F28 94F A 203 18.495 -5.026 20.445 1.00 33.49 F ATOM 1416 CL 94F A 203 19.224 -0.960 23.165 1.00 29.22 CL
change and make the numbering and naming consistent:
cat 94F.pdb
ATOM 1382 CA LIG A 203 29.215 -1.013 17.747 1.00 23.10 C ATOM 1383 CB LIG A 203 30.264 -1.172 18.849 1.00 23.68 C ATOM 1384 SG LIG A 203 29.632 -1.020 20.503 1.00 25.01 S ATOM 1385 C31 LIG A 203 16.511 -4.125 24.817 1.00 32.17 C ATOM 1386 C30 LIG A 203 15.606 -4.260 23.787 1.00 32.36 C ATOM 1387 C32 LIG A 203 17.840 -3.910 24.531 1.00 31.54 C ATOM 1388 C29 LIG A 203 16.037 -4.183 22.484 1.00 32.47 C ATOM 1389 C19 LIG A 203 21.614 -2.199 22.881 1.00 29.12 C ATOM 1390 C5 LIG A 203 23.964 -5.464 22.540 1.00 29.57 C ATOM 1391 C18 LIG A 203 22.453 -3.293 22.771 1.00 29.13 C ATOM 1392 C23 LIG A 203 18.284 -3.829 23.223 1.00 31.43 C ATOM 1393 C22 LIG A 203 19.692 -3.612 23.019 1.00 29.79 C ATOM 1394 C24 LIG A 203 17.372 -3.972 22.203 1.00 32.05 C ATOM 1395 C3 LIG A 203 21.900 -4.565 22.770 1.00 29.39 C ATOM 1396 C2 LIG A 203 20.533 -4.693 22.895 1.00 29.45 C ATOM 1397 C20 LIG A 203 20.247 -2.347 23.012 1.00 29.51 C ATOM 1398 C7 LIG A 203 23.836 -3.189 22.644 1.00 28.94 C ATOM 1399 C14 LIG A 203 29.536 0.583 20.690 1.00 25.47 C ATOM 1400 C13 LIG A 203 28.376 1.143 21.474 1.00 26.40 C ATOM 1401 C12 LIG A 203 27.093 0.850 20.795 1.00 26.10 C ATOM 1402 C9 LIG A 203 23.979 -0.953 21.731 1.00 28.62 C ATOM 1403 C17 LIG A 203 25.969 -2.149 22.595 1.00 29.17 C ATOM 1404 C10 LIG A 203 25.024 -0.390 20.794 1.00 28.12 C ATOM 1405 C16 LIG A 203 26.678 -0.809 22.586 1.00 28.22 C ATOM 1406 C25 LIG A 203 17.826 -3.897 20.794 1.00 32.91 C ATOM 1407 N4 LIG A 203 22.652 -5.665 22.653 1.00 29.29 N ATOM 1408 N6 LIG A 203 24.595 -4.289 22.534 1.00 29.70 N ATOM 1409 N8 LIG A 203 24.523 -1.948 22.642 1.00 29.33 N ATOM 1410 N11 LIG A 203 26.238 0.005 21.476 1.00 27.18 N ATOM 1411 O15 LIG A 203 26.847 1.362 19.713 1.00 25.34 O ATOM 1412 F1 LIG A 203 19.995 -5.935 22.878 1.00 29.69 F ATOM 1413 F26 LIG A 203 16.791 -3.770 19.931 1.00 34.77 F ATOM 1414 F27 LIG A 203 18.674 -2.862 20.538 1.00 31.92 F ATOM 1415 F28 LIG A 203 18.495 -5.026 20.445 1.00 33.49 F ATOM 1416 CL LIG A 203 19.224 -0.960 23.165 1.00 29.22 CL
Uses chimera to add hydrogens:
a co-factory (gdp), gdp.pdb:
and a receptor, rec.pdb:
Here is a modified cystiene residue (this is without a charge and without a hydrogen):
cat CYM.prep
0 0 2
CYSTEINE without h and without charge for covalent
CYM INT 0
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
5 H H E 4 3 2 1.010 119.800 0.000 0.27190
6 CA CX M 4 3 2 1.449 121.900 180.000 0.02130
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.11240
8 CB 2C 3 6 4 3 1.525 111.100 60.000 -0.12310
9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.11120
10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.11120
11 SG SH E 8 6 4 1.810 116.000 180.000 -0.23580
12 C C M 6 4 3 1.522 111.100 180.000 0.59730
13 O O E 12 6 4 1.229 120.500 0.000 -0.56790
IMPROPER
-M CA N H
CA +M C O
DONE
STOP