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