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UCL-CCS / TIES

Topology Superimposition based on joint graph traversal
MIT License
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leaprc.protein.ff19SB: not found #303

Closed adw62 closed 2 years ago

adw62 commented 2 years ago

When I'm using the command line with latest code like this 'ties create -l ligand.mol2 l_H18.mol2 -p receptor.pdb -nc 1' I get

/home/cdt1605/miniconda3/envs/TIES_loc/bin/teLeap: Fatal Error! Could not open file leaprc.protein.ff19SB: not found

Do you see the same or have I messed up my env? Adding the cmd argument -pff 'leaprc.protein.ff14SB' resolves the problem.

adw62 commented 2 years ago

Even weirder on the command line I do not see the spurious bond hahah

So we can double check whats going on this is the input I'm using: err.zip

Should be the same as before but just in case.

adw62 commented 2 years ago

Okay my /home/cdt1605/miniconda3/envs/TIES_loc/dat/leap/cmd/ dir does not contain leaprc.protein.ff19SB. Question is can this happen to other user? Not sure what caused it for me.

adw62 commented 2 years ago

Maybe ignore this, an Ambertools reinstall fixed the problem. Was interesting the spurious bond did not occur on the command line though, a clue perhaps, or more evidence my conda environments are a mess?