auto prepare top example

[xy21hb]

Any example on how to use prepare_dual_topology.py to generate gmx top file for ligands? The manual says it uses AcPYPE, but if I have a list of ligands, can I generate the top files at once by prepare_dual_topology.py? If yes, what flags in the cmd line could I use?

[luancarvalhomartins]

Dear @xy21hb,

It should be quite straightforward. Just pass --parameterize=acpype to prepare_dual_topology.py (other --parameterize_* options are worth taking a look).

Sorry the manual was not clear enough. I will improve that section.

[xy21hb]

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, in local_print formatted_string = '\n{:=^50}\n{}{:=^50}\n'.format(' STACK INFO ', ''.join(traceback.format_stack()), =================== STACK INFO =================== [ERROR] Argument "--structure" or config file option "structure" is required. Please see the documentation

I see "--structure" is for ""Solvated and equilibrated system or receptor structure", but I am just dealing with the ligand only.

[xy21hb]

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' File "/home/yxu/PyAutoFEP-master/os_util.py", line 307, in local_print formatted_string = '\n{:=^50}\n{}{:=^50}\n'.format(' STACK INFO ', ''.join(traceback.format_stack()), =================== STACK INFO =================== [ERROR] Argument "--structure" or config file option "structure" is required. Please see the documentation

I see "--structure" is for "Solvated and equilibrated system or receptor structure", but I am just dealing with the ligand only to get FXR_12.itp.

Best, Yao

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From: Luan Carvalho Martins @.> Sent: Tuesday, August 1, 2023 2:41 AM To: luancarvalhomartins/PyAutoFEP @.> Cc: xy21hb @.>; Mention @.> Subject: Re: [luancarvalhomartins/PyAutoFEP] auto prepare top example (Issue #105)

Dear @xy21hbhttps://github.com/xy21hb,

It should be quite straightforward. Just pass --parameterize=acpype to prepare_dual_topology.py (other --parameterize_* options are worth taking a look).

Sorry the manual was not clear enough. I will improve that section.

— Reply to this email directly, view it on GitHubhttps://github.com/luancarvalhomartins/PyAutoFEP/issues/105#issuecomment-1659396926, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADM4TWT7Y3AVIEJXFXAZJALXTBGDLANCNFSM6AAAAAA25Q6FGE. You are receiving this because you were mentioned.Message ID: @.***>

[luancarvalhomartins]

prepare_dual_topology.py will parameterize ligands, then proceed to pairs, system building etc as usual. Add every option you will need to prepare your perturbations, everything. Instead of passing the ligand topologies, use --parameterize=acpype.

[xy21hb]

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！

[xy21hb]

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, 74,76, 84, ...., to get the corresponding .itp files for the subsequent steps? Many thanks！

Best, Yao

---

From: Luan Carvalho Martins @.> Sent: Tuesday, August 1, 2023 2:41 AM To: luancarvalhomartins/PyAutoFEP @.> Cc: xy21hb @.>; Mention @.> Subject: Re: [luancarvalhomartins/PyAutoFEP] auto prepare top example (Issue #105)

Dear @xy21hbhttps://github.com/xy21hb,

It should be quite straightforward. Just pass --parameterize=acpype to prepare_dual_topology.py (other --parameterize_* options are worth taking a look).

Sorry the manual was not clear enough. I will improve that section.

— Reply to this email directly, view it on GitHubhttps://github.com/luancarvalhomartins/PyAutoFEP/issues/105#issuecomment-1659396926, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADM4TWT7Y3AVIEJXFXAZJALXTBGDLANCNFSM6AAAAAA25Q6FGE. You are receiving this because you were mentioned.Message ID: @.***>

[luancarvalhomartins]

Sorry for the tardiness.

Sure, I cooked an quick example of how to use parameterization. Note that this example also uses the vina pose loader (pose_loader = vina) and reading a perturbation map from a file (perturbation_map = pertmap.txt), which are not related to the parameterization. These are the options you may want to take a look:

# Use automatic parameterization via AcPYPE (currently, this is the only backend supported )
parameterize = acpype
# Save ligand topologiesto this dir
parameterize_output_dir = lig_topologies

parameterize.zip