Unfortunately, the answer is that right now you don’t - ISOLDE currently only helps you parameterise new organic ligands that *aren’t* covalently bonded to anything else. We’re currently discussing a new, much more general solution, but for now you’d really need to recruit the help of a force field specialist to get that happening. If you *do* know someone who can help you parameterise this residue for AMBER, get back to me and I can talk you through incorporating it into ISOLDE’s force field.

Best, Tristan

On Tue, 25 Jul 2023 at 16:17, Trevor Sewell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Hi Everyone,

I am adding residues (essentially modified cysteines ) to the polypeptide chain.

e.g.

HETATM 1 N2 PGR 0 1.743 -1.624 -0.731 1.00 0.00 N

HETATM 2 C1 PGR 0 -0.077 -0.207 -0.018 1.00 0.00 C

HETATM 3 C2 PGR 0 1.394 -0.544 0.203 1.00 0.00 C

HETATM 4 C3 PGR 0 -0.485 0.927 -0.717 1.00 0.00 C

HETATM 5 C4 PGR 0 -1.034 -1.073 0.503 1.00 0.00 C

HETATM 6 C5 PGR 0 -1.840 1.189 -0.887 1.00 0.00 C

HETATM 7 C6 PGR 0 -2.389 -0.810 0.331 1.00 0.00 C

HETATM 8 C7 PGR 0 -2.794 0.323 -0.364 1.00 0.00 C

HETATM 9 C8 PGR 0 2.379 0.585 -0.085 1.00 0.00 C

HETATM 10 H1 PGR 0 1.529 -0.961 1.213 1.00 0.00 H

HETATM 11 H2 PGR 0 0.232 1.599 -1.120 1.00 0.00 H

HETATM 12 H3 PGR 0 -0.727 -1.940 1.035 1.00 0.00 H

HETATM 13 H4 PGR 0 -2.145 2.053 -1.418 1.00 0.00 H

HETATM 14 H5 PGR 0 -3.116 -1.477 0.733 1.00 0.00 H

HETATM 15 H6 PGR 0 -3.837 0.527 -0.497 1.00 0.00 H

HETATM 16 H7 PGR 0 1.655 -1.298 -1.705 1.00 0.00 H

HETATM 17 H8 PGR 0 1.143 -2.449 -0.581 1.00 0.00 H

HETATM 18 O18 PGR 0 3.393 0.026 -0.528 1.00 0.00 O

HETATM 19 SG PGR 0 2.777 1.511 1.356 1.00 0.00 S

HETATM 20 CB PGR 0 1.349 2.524 1.801 1.00 0.00 C

HETATM 21 CA PGR 0 1.698 3.446 2.926 1.00 0.00 C

HETATM 22 N PGR 0 0.565 4.254 3.182 1.00 0.00 N

HETATM 23 C PGR 0 2.646 4.407 2.450 1.00 0.00 C

HETATM 24 O24 PGR 0 2.145 5.309 1.717 1.00 0.00 O

HETATM 25 O25 PGR 0 3.976 4.409 2.828 1.00 0.00 O

HETATM 26 H9 PGR 0 1.980 1.252 -0.806 1.00 0.00 H

HETATM 27 H11 PGR 0 1.044 3.140 0.942 1.00 0.00 H

HETATM 28 H12 PGR 0 0.527 1.867 2.099 1.00 0.00 H

HETATM 29 H13 PGR 0 2.043 2.881 3.803 1.00 0.00 H

HETATM 30 H14 PGR 0 -0.245 3.721 3.480 1.00 0.00 H

HETATM 31 H15 PGR 0 0.359 4.821 2.336 1.00 0.00 H

TER

My question is: How do I set up Isolde so that it can refine the structure?

Many thanks,

Trevor Sewell

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