DAL isn't a different ligand, it's just different coordinates. You can use
ALA parameters for it as long as your input coordinates properly have it
set to the D isomer. See for example
Experimental and Computational Analysis of Protein Stabilization by
Gly-to-D-Ala Substitution: A Convolution of Native State and Unfolded State
Effects. Zou, J., Song, B., Simmerling, C., Raleigh, D., Journal of the
American Chemical Society, 2016, 138 (48), 15682–15689
I'm not aware of any existing ACB parameters. I would suggest capping it to
the dipeptide (acetylate and amidate) and using that to generate partial
charges. From there you can treat it as a ligand, but if you end up using
GAFF atom types then you need the cross terms between GAFF and the protein
force field in order to model the backbone. Also, GAFF types for the
backbone would not use the existing protein parameters, which have been
highly optimized over the years. I think you'd be better off using the
standard protein atom types for the backbone, perhaps adapting GAFF for the
side chain. It's small enough that following the ff14SB protocol to
optimize the side chain rotational profiles wouldn't be that difficult. Not
a trivial exercise, though. Maybe someone else here knows of automated
tools for this.
On Mon, Oct 18, 2021 at 4:07 PM Nagar, Hemant <hn533621.ohio.edu> wrote:
> 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 - 14:00:02 PDT
