On Fri, Dec 22, 2023, Bennion, Brian wrote:
>
>We are parameterizing thousand small molecules for projects and every once
>and awhile come across a bridged cyclcobutyl group in this compounds.
>We use antechamber to operate on mol2 files as found in this code https://github.com/XiaohuaZhangLLNL/conveyorlc
>
>Unfortunately I can't share the exact compound but a snippet of leap.out is
>given below. I believe this is due to conversion issues within antechamber
>as the structure that comes out contains dummy atoms
I don't know where the dummy atoms are coming from. Can you make a simple
example of a bridged cyclobutyl compound whose PDB or mol2 file you would be
able to share? (Even before doing that, try running antechamber with a PDB
file as input, rather than a mol2 file, if indeed you were using a mol2 file
for input.)
Without some way to run an example ourselves, just having the leap.log file
doesn't allow us to help very much.
....dac
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Received on Fri Dec 29 2023 - 10:30:02 PST
