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Compound included in residue list #30

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agrazzi opened this issue Mar 24, 2023 · 0 comments
Open

Compound included in residue list #30

agrazzi opened this issue Mar 24, 2023 · 0 comments

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@agrazzi
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agrazzi commented Mar 24, 2023

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 agrazzi changed the title Lipid included in protein Compound included in residue list Mar 24, 2023
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