On Wed, Jun 09, 2021, Bhattacharjee, Sinjini wrote:
>Hello, I have been trying to clean up a pdb file after adding hydrogens
>from the H++ server.
You PDB file is really messed up. I'm not sure whether you did this, or it
is the result of the H++ server. PDB ATOM records have data in partiulcar
columns. Your file starts like this:
ATOM 1 N VAL 1 13.975 44.824 -8.191 1.00 0.00 N
ATOM 2 H1 VAL 1 14.347 45.427 -8.914 1.00 0.00 H
but a correct ATOM record should look like this:
ATOM 11 C8 G B 15 1.794 2.345 20.675 1.00 68.35 C
You residue names are in columns 19-21 instead of 18-20; you x-coordinates
are in columns 32-39 instead of 31-38, etc.
You might want to start over, or use a text editor to fix the format of your
PDB file.
...good luck...dac
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Received on Wed Jun 09 2021 - 07:30:03 PDT
