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Compound included in residue list

Open agrazzi opened this issue 2 years ago • 0 comments

I'm simulating a CG version (Martini3) of a Glycine-Receptor in a POPC membrane with some THC molecules that I've parameterized myself. When I try to run the demo script that you have so kindly provided on this website, I've noticed that compound I'm interested in, THC, is included in the residue list that I suppose should contain only the amminoacids of the protein, so instead of the 1730 residues I obtain 1746:

COLLECT INTERACTIONS FROM TRAJECTORIES: 100%|█████████████████████████████████████████████████| 1/1 [00:15<00:00, 15.35s/it] Residue Residue ID 0 1PRO 0 1 2MET 1 2 3PRO 2 3 4PRO 3 4 5SER 4 ... ... ... 1741 2079THC 1741 1742 2080THC 1742 1743 2081THC 1743 1744 2082THC 1744 1745 2083THC 1745

[1746 rows x 2 columns]

This of course leads to problems down the line, given that it expects some information regarding the residue 'THC' which of course are present in the program's library.

CALCULATE BINDING SITE SURFACE AREA: 100%|████████████████████████████████████████████████████| 1/1 [00:26<00:00, 26.85s/it] Creating new director: /home/agrazzi/Desktop/THC/THC_map4/CHARMM/GlyR/Trial38/run9/test/Interaction_THC/Dataset_THC Traceback (most recent call last): File "/home/agrazzi/Desktop/THC/THC_map4/CHARMM/GlyR/Trial38/run9/test/script_mod.py", line 100, in li.write_site_info(sort_residue="Residence Time") File "/home/agrazzi/miniconda3/lib/python3.10/site-packages/pylipid/api/api.py", line 1865, in write_site_info text = self._format_BS_print_info(bs_id, nodes, sort_residue) File "/home/agrazzi/miniconda3/lib/python3.10/site-packages/pylipid/api/api.py", line 1981, in _format_BS_print_info res_stats[Residue_property_book[re.findall("[a-zA-Z]+$", residue)[0]]] += 1 KeyError: 'THC'

Is there a way to properly exclude the compound of interest, "THC", from the residue list?

Thanks in advance for you support

P.s. please find attached .gro and a truncated trajectory .xtc

test_truncated.xtc.txt test.gro.txt

agrazzi avatar Mar 24 '23 11:03 agrazzi