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1. This problem is due to the special form of mol2 generated by obabel, which can be omitted by either correcting the format or generated by other tools, e.g. Maestro....

Error msg is below, some steps of structures are not stable, and GMX fails to collect edr energy files  

Though I have not checked the structure, I believe it is due to some unstable ligs since the system is a large membrane protein. Running with --no_checks would give the...

prepare_dual_topology.py --input_ligands ../FXR_12.mol --parameterize=acpype =================== STACK INFO =================== File "/home/yxu/PyAutoFEP-master/docs/tutorial01/lig_data/testop/../../../../prepare_dual_topology.py", line 3648, in os_util.local_print('Argument "--{}" or config file option "{}" is required. Please see the documentation' File "/home/yxu/PyAutoFEP-master/os_util.py", line 307,...

Dear Luan, I used prepare_dual_topology.py --input_ligands ../FXR_12.mol --parameterize=acpype =================== STACK INFO =================== File "/home/yxu/PyAutoFEP-master/docs/tutorial01/lig_data/testop/../../../../prepare_dual_topology.py", line 3648, in os_util.local_print('Argument "--{}" or config file option "{}" is required. Please see the documentation'...

could you provide the example, as in the tutorial, how could one parameterize the FXR_12, 74,76, 84, ...., to get the corresponding .itp files for the subsequent steps? Many thanks！

Dear Luan, I reread the tutorial and manual but could not sort out the way. Could you kindly provide the example, as in the tutorial, how to parameterize the FXR_12,...

If you are running Tutorial example, just check /PyAutoFEP-master/docs/tutorial01/tutorial/FXR_12-FXR_74/water/md/feprun_..._14082023.log or similar file.

check your loading modules, I guess there are some modules missing, esp. those related to gmx

 Change the Gromacs version to the designated.