On Sat, Aug 29, 2020, Jatin Kashyap wrote:
>
>I am trying to perform MD run on a ligand-receptor complex after
>splitting and preparing them individually in PyMol from a RCSB downloaded
>version.
I'm not sure what you/PyMol did, but it looks like there are problems
with your PDB file:
>Created a new atom named: HA2 within residue: .R<GLU 54>
>Created a new atom named: HA3 within residue: .R<GLU 54>
This says that atoms with the above name are in the PDB file, but GLU
would never have such atoms.
>Created a new atom named: HG1 within residue: .R<LYS 79>
Same type of problem: LYS doesn't have an HG1 atom.
You can strip all the hydrogens and try again, but I fear that other
problems (missing atoms) may have crept in as well. Why do you need
PyMol in this workflow?
....dac
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Received on Sat Aug 29 2020 - 10:30:02 PDT
