--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Apr 23, 2024, at 1:19 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thank you very much Elaine !

Indeed the preparation of DNA is a bit tricky, since there is no automatic way to fix the structure as in the case of adding missed hydrogens for a protein as you mentioned.

In this case, I took another complex contained a shorter fragment of DNA (with the similar problem related to the tleap parametrization), I could resolve the issue via deleting the last three atoms from the first residues of the DNA. So this was the original:

ATOM 1 HO5' DC5 1 1.764 17.930 5.183 1.00 0.00 H
ATOM 2 O5' DC5 1 2.181 17.899 4.319 1.00 0.00 O
ATOM 3 C5' DC5 1 2.302 19.107 3.565 1.00 0.00 C
ATOM 4 H5' DC5 1 2.901 19.819 4.134 1.00 0.00 H
ATOM 5 H5'' DC5 1 1.316 19.532 3.375 1.00 0.00 H
ATOM 6 C4' DC5 1 2.984 18.826 2.246 1.00 0.00 C
ATOM 7 H4' DC5 1 3.057 19.731 1.642 1.00 0.00 H
ATOM 8 O4' DC5 1 4.361 18.445 2.497 1.00 0.00 O
ATOM 9 C1' DC5 1 4.629 17.185 1.899 1.00 0.00 C
ATOM 10 H1' DC5 1 5.236 17.362 1.011 1.00 0.00 H
ATOM 11 N1 DC5 1 5.524 16.432 2.787 1.00 0.00 N
ATOM 12 C6 DC5 1 5.172 16.185 4.084 1.00 0.00 C
ATOM 13 H6 DC5 1 4.261 16.606 4.484 1.00 0.00 H
ATOM 14 C5 DC5 1 5.938 15.427 4.875 1.00 0.00 C
ATOM 15 H5 DC5 1 5.625 15.238 5.902 1.00 0.00 H
ATOM 16 C4 DC5 1 7.137 14.898 4.317 1.00 0.00 C
ATOM 17 N4 DC5 1 7.922 14.108 5.051 1.00 0.00 N
ATOM 18 H41 DC5 1 8.764 13.752 4.621 1.00 0.00 H
ATOM 19 H42 DC5 1 7.670 13.882 6.003 1.00 0.00 H
ATOM 20 N3 DC5 1 7.511 15.163 3.063 1.00 0.00 N
ATOM 21 C2 DC5 1 6.729 15.934 2.273 1.00 0.00 C
ATOM 22 O2 DC5 1 7.050 16.216 1.107 1.00 0.00 O
ATOM 23 C3' DC5 1 2.353 17.665 1.476 1.00 0.00 C
ATOM 24 H3' DC5 1 1.351 17.422 1.830 1.00 0.00 H
ATOM 25 C2' DC5 1 3.282 16.503 1.754 1.00 0.00 C
ATOM 26 H2' DC5 1 2.732 15.712 2.264 1.00 0.00 H
ATOM 27 H2'' DC5 1 3.679 16.121 0.813 1.00 0.00 H
ATOM 28 O3' DC5 1 2.322 17.915 0.072 1.00 0.00 O
ATOM 29 P DC5 1 0.997 17.702 5.368 1.00 0.00 P
ATOM 30 OP1 DC5 1 -0.278 17.623 4.612 1.00 0.00 O
ATOM 31 OP2 DC5 1 1.374 16.596 6.287 1.00 0.00 O

and tleap sent an error about these unknown atoms P, OP1, OP2. After they were removed, everything works, and here the output pdb for the tleap ( I show only the first two residues of the DNA first chain):

CRYST1 101.813 101.813 101.813 109.47 109.47 109.47 P 1 1
ATOM 1 HO5' DC5 1 -12.492 1.952 13.803 1.00 0.00
ATOM 2 O5' DC5 1 -11.735 2.474 14.076 1.00 0.00
ATOM 3 C5' DC5 1 -11.927 3.534 15.016 1.00 0.00
ATOM 4 H5' DC5 1 -12.321 3.115 15.943 1.00 0.00
ATOM 5 H5'' DC5 1 -12.632 4.265 14.619 1.00 0.00
ATOM 6 C4' DC5 1 -10.610 4.218 15.299 1.00 0.00
ATOM 7 H4' DC5 1 -10.741 5.050 15.991 1.00 0.00
ATOM 8 O4' DC5 1 -9.740 3.295 16.004 1.00 0.00
ATOM 9 C1' DC5 1 -8.512 3.159 15.302 1.00 0.00
ATOM 10 H1' DC5 1 -7.751 3.709 15.856 1.00 0.00
ATOM 11 N1 DC5 1 -8.073 1.762 15.403 1.00 0.00
ATOM 12 C6 DC5 1 -8.883 0.745 14.979 1.00 0.00
ATOM 13 H6 DC5 1 -9.883 0.963 14.632 1.00 0.00
ATOM 14 C5 DC5 1 -8.460 -0.523 14.985 1.00 0.00
ATOM 15 H5 DC5 1 -9.124 -1.310 14.630 1.00 0.00
ATOM 16 C4 DC5 1 -7.140 -0.772 15.458 1.00 0.00
ATOM 17 N4 DC5 1 -6.654 -2.015 15.455 1.00 0.00
ATOM 18 H41 DC5 1 -5.714 -2.153 15.798 1.00 0.00
ATOM 19 H42 DC5 1 -7.219 -2.781 15.117 1.00 0.00
ATOM 20 N3 DC5 1 -6.353 0.207 15.910 1.00 0.00
ATOM 21 C2 DC5 1 -6.793 1.486 15.902 1.00 0.00
ATOM 22 O2 DC5 1 -6.098 2.422 16.329 1.00 0.00
ATOM 23 C3' DC5 1 -9.859 4.630 14.032 1.00 0.00
ATOM 24 H3' DC5 1 -10.502 4.651 13.152 1.00 0.00
ATOM 25 C2' DC5 1 -8.812 3.549 13.867 1.00 0.00
ATOM 26 H2' DC5 1 -8.968 3.035 12.919 1.00 0.00
ATOM 27 H2'' DC5 1 -7.819 4.000 13.878 1.00 0.00
ATOM 28 O3' DC5 1 -9.211 5.891 14.187 1.00 0.00
ATOM 29 P DC 2 -8.364 6.496 12.962 1.00 0.00
ATOM 30 OP1 DC 2 -8.616 7.960 12.930 1.00 0.00
ATOM 31 OP2 DC 2 -8.638 5.674 11.754 1.00 0.00
ATOM 32 O5' DC 2 -6.848 6.247 13.385 1.00 0.00
ATOM 33 C5' DC 2 -6.315 6.819 14.579 1.00 0.00
ATOM 34 H5' DC 2 -6.763 6.307 15.432 1.00 0.00
ATOM 35 H5'' DC 2 -6.546 7.883 14.632 1.00 0.00
ATOM 36 C4' DC 2 -4.817 6.632 14.619 1.00 0.00
ATOM 37 H4' DC 2 -4.402 7.131 15.495 1.00 0.00
ATOM 38 O4' DC 2 -4.508 5.232 14.820 1.00 0.00
ATOM 39 C1' DC 2 -3.694 4.748 13.763 1.00 0.00
ATOM 40 H1' DC 2 -2.678 4.608 14.133 1.00 0.00
ATOM 41 N1 DC 2 -4.136 3.383 13.438 1.00 0.00
ATOM 42 C6 DC 2 -5.384 3.158 12.927 1.00 0.00
ATOM 43 H6 DC 2 -6.063 3.986 12.781 1.00 0.00
ATOM 44 C5 DC 2 -5.786 1.924 12.600 1.00 0.00
ATOM 45 H5 DC 2 -6.785 1.777 12.192 1.00 0.00
ATOM 46 C4 DC 2 -4.867 0.857 12.808 1.00 0.00
ATOM 47 N4 DC 2 -5.208 -0.393 12.488 1.00 0.00
ATOM 48 H41 DC 2 -4.528 -1.121 12.650 1.00 0.00
ATOM 49 H42 DC 2 -6.119 -0.588 12.097 1.00 0.00
ATOM 50 N3 DC 2 -3.651 1.063 13.320 1.00 0.00
ATOM 51 C2 DC 2 -3.258 2.316 13.647 1.00 0.00
ATOM 52 O2 DC 2 -2.137 2.544 14.131 1.00 0.00
ATOM 53 C3' DC 2 -4.110 7.044 13.329 1.00 0.00
ATOM 54 H3' DC 2 -4.717 7.693 12.699 1.00 0.00
ATOM 55 C2' DC 2 -3.871 5.726 12.616 1.00 0.00
ATOM 56 H2' DC 2 -4.391 5.732 11.658 1.00 0.00
ATOM 57 H2'' DC 2 -2.803 5.591 12.449 1.00 0.00
ATOM 58 O3' DC 2 -2.873 7.696 13.614 1.00 0.00

.... etc

Now it looks OK visually and I will test the structure in simulation. By the way, it would be great to have a tool in Chimera-X that automatically recognises problems with DNA structures.

Yours with thanks

Enrico

Il giorno lun 22 apr 2024 alle ore 18:57 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
I don't know what atoms exactly are missing. You would probably need to use the interactive building tool and add atoms one at a time, modify their atom types, etc. This would show the commands in the Log, but it would be too hard to figure out the commands without using the interactive graphical tool first. I.e. even if I knew exactly which atoms were missing, I would still use the graphical tool.

Menu: Tools.. Structure Editing... Build Structure. See the Modify Structure section.

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#modify>

To fix problems that require your interactive visual understanding, especially when different structures have different problems, it is not possible to make general scripts that will do everything without your oversight.

Also in this case you need to figure out what Amber considers to be the complete residue (which atoms must be present and therefore which ones you have to add, what the correct names are for the atoms and residue, etc.).

The Dock Prep and Add Hydrogens tools have built-in features to correct missing sidechains and OXT atoms of peptides, but they do not do this for nucleic acids.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 22, 2024, at 9:33 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear Chimera-X users
>
> I am preparing the structure of the protein-DNA complex for molecular dynamics simulation with Amber. This is the original pdb:
> https://www.rcsb.org/structure/5FKW
>
> When I try to parametrize it the tleap shows the following error because of the absence of some atoms from the phosphate:
>
> FATAL: Atom .R<DG5 733>.A<P 32> does not have a type.
> FATAL: Atom .R<DG5 733>.A<OP1 33> does not have a type.
> FATAL: Atom .R<DG5 733>.A<OP2 34> does not have a type.
> FATAL: Atom .R<DG5 758>.A<P 32> does not have a type.
> FATAL: Atom .R<DG5 758>.A<OP1 33> does not have a type.
> FATAL: Atom .R<DG5 758>.A<OP2 34> does not have a type.
>
> Would it be possible to use some commands of the Chimera-X to automatically repair this part of the DNA by adding missing atoms ?
>
> Thank you in advance !
>
> Enrico

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