Hi All,
I want to generate force field parameters for nonstandard residues . Currently, I am taking out the particular fragment from the pdb file and saving it to different file. After that I am generating the parameter using antechamber. Do I need to cap the terminals of fragments before running it to antechamber or Is there any particular procedure for generating FF parameters? Here is the some portion of my pdb file for reference purpose. I want to generate parameters for DAL and ACB residue.
ATOM 1 N DAL A 1 7.379 3.883 3.167 1.00 0.00 N
ATOM 2 CA DAL A 1 8.241 3.023 2.496 1.00 0.00 C
ATOM 3 CB DAL A 1 8.563 3.385 1.040 1.00 0.00 C
ATOM 4 C DAL A 1 8.174 1.567 2.779 1.00 0.00 C
ATOM 5 O DAL A 1 8.741 0.695 2.148 1.00 0.00 O
ATOM 6 H1 DAL A 1 6.578 3.469 3.618 1.00 0.00 H
ATOM 7 HA DAL A 1 9.296 2.919 2.206 1.00 0.00 H
ATOM 8 HB1 DAL A 1 8.948 2.559 0.423 1.00 0.00 H
ATOM 9 HB2 DAL A 1 9.239 4.246 0.927 1.00 0.00 H
ATOM 10 HB3 DAL A 1 7.638 3.690 0.546 1.00 0.00 H
ATOM 11 N LEU A 2 7.402 1.250 3.848 1.00 0.00 N
ATOM 12 CA LEU A 2 7.176 -0.043 4.325 1.00 0.00 C
ATOM 13 C LEU A 2 6.362 -0.988 3.499 1.00 0.00 C
ATOM 14 O LEU A 2 6.128 -2.151 3.766 1.00 0.00 O
ATOM 15 CB LEU A 2 7.066 -0.290 5.819 1.00 0.00 C
ATOM 16 CG LEU A 2 8.074 0.521 6.677 1.00 0.00 C
ATOM 17 CD1 LEU A 2 7.768 0.327 8.178 1.00 0.00 C
ATOM 18 CD2 LEU A 2 9.532 0.107 6.376 1.00 0.00 C
ATOM 19 H LEU A 2 7.094 2.017 4.429 1.00 0.00 H
ATOM 20 HA LEU A 2 7.834 -0.925 4.279 1.00 0.00 H
ATOM 21 HB2 LEU A 2 6.055 -0.025 6.134 1.00 0.00 H
ATOM 22 HB3 LEU A 2 7.176 -1.352 6.066 1.00 0.00 H
ATOM 23 HG LEU A 2 7.964 1.585 6.455 1.00 0.00 H
ATOM 24 HD11 LEU A 2 6.751 0.653 8.408 1.00 0.00 H
ATOM 25 HD12 LEU A 2 7.866 -0.723 8.464 1.00 0.00 H
ATOM 26 HD13 LEU A 2 8.456 0.916 8.789 1.00 0.00 H
ATOM 27 HD21 LEU A 2 9.787 0.300 5.332 1.00 0.00 H
ATOM 28 HD22 LEU A 2 10.227 0.676 6.999 1.00 0.00 H
ATOM 29 HD23 LEU A 2 9.685 -0.956 6.577 1.00 0.00 H
ATOM 30 C ACB A 3 4.131 -2.031 1.537 1.00 0.00 C
ATOM 31 O ACB A 3 3.732 -2.524 2.571 1.00 0.00 O
ATOM 32 OXT ACB A 3 3.537 -2.348 0.412 1.00 0.00 O
ATOM 33 CA ACB A 3 4.944 -0.791 1.420 1.00 0.00 C
ATOM 34 N ACB A 3 5.819 -0.372 2.421 1.00 0.00 N
ATOM 35 CB ACB A 3 4.537 0.266 0.500 1.00 0.00 C
ATOM 36 CG ACB A 3 3.178 0.883 0.618 1.00 0.00 C
ATOM 37 C4 ACB A 3 5.557 1.343 0.130 1.00 0.00 C
ATOM 38 OD2 ACB A 3 2.727 1.777 -0.078 1.00 0.00 O
ATOM 39 HA ACB A 3 5.395 -0.923 0.426 1.00 0.00 H
ATOM 40 H ACB A 3 6.182 0.559 2.282 1.00 0.00 H
ATOM 41 HB3 ACB A 3 4.206 0.247 -0.554 1.00 0.00 H
ATOM 42 H41 ACB A 3 5.286 1.916 -0.763 1.00 0.00 H
ATOM 43 H42 ACB A 3 6.545 0.913 -0.055 1.00 0.00 H
ATOM 44 H43 ACB A 3 5.661 2.061 0.946 1.00 0.00 H
ATOM 45 N ARG A 4 2.504 0.459 1.718 1.00 0.00 N
ATOM 46 CA ARG A 4 1.279 0.889 2.229 1.00 0.00 C
ATOM 47 C ARG A 4 0.833 0.383 3.549 1.00 0.00 C
ATOM 48 O ARG A 4 -0.145 0.799 4.137 1.00 0.00 O
ATOM 49 CB ARG A 4 0.097 1.223 1.299 1.00 0.00 C
ATOM 50 CG ARG A 4 -0.495 -0.035 0.615 1.00 0.00 C
Regards,
Hemant Nagar
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Received on Mon Oct 18 2021 - 13:30:02 PDT
