Hi,
I used the following command with babel
babel -isdf library.sdf -omol2 library\molecule.mol2 -meh -p7.3 -b -c
--gen3D --minimize --ffGAFF --steps5000
My library contains > 50 000 molecules
I get the following messages
WARNING: damped steplength 2.02315e-21 to 1.32823e-21 (several of these,
953 to be exact)
and 10927 times
WARNING: too small "scale" at Newton2NumLineSearch
Babel stops after it gets to the 424th molecule and I have no idea why.
Thanks for your help,
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