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:
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