Hi,
Thank you for the valuable comments.
After checking, the pdb file did not exist in the working directory. So,
it was my simple mistake.
Anyway, I got it to work.
Thank you,
Kohsei Tsuji
On 2017/08/24 2:01, Geoffrey Hutchison wrote:
I think my first question is whether 3upo_protein.pdb exists in the directory.
If so, can Open Babel read it on the command line?
obabel 3upo_protein.pdb -O 3upo.mol2
# this will attempt to convert the PDB file to Mol2
-Geoff
--receptor 3upo_protein.pdb\
--residue B:SER222\
--outputfile ligcovalent.pdb
==============================
*** Open Babel Error in ReadFile
Cannot read from 3upo_protein.pdb
[ ERROR ] Fail to read molecule "3upo_protein.pdb"
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