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do-order-milti.py for POPC
- mbusahit
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7 years 8 months ago #5792
by mbusahit
do-order-milti.py for POPC was created by mbusahit
Hi all,
I am trying to calculate order parameter for POPC bilayer using do-order-milti.py script. I encounter the following error -
Starting P2 calculationTaking care of snapshot frame_dump_0.gro
Traceback (most recent call last):
File "do-order-multi.py", line 150, in <module>
vector[j] = first[j] - second[j]
IndexError: list index out of range
The script works well for other lipids. Why does it not work for POPC ?
I am trying to calculate order parameter for POPC bilayer using do-order-milti.py script. I encounter the following error -
Starting P2 calculationTaking care of snapshot frame_dump_0.gro
Traceback (most recent call last):
File "do-order-multi.py", line 150, in <module>
vector[j] = first[j] - second[j]
IndexError: list index out of range
The script works well for other lipids. Why does it not work for POPC ?
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- tsjerk
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7 years 8 months ago #5810
by tsjerk
Replied by tsjerk on topic do-order-milti.py for POPC
Hi,
In the script, the lipids are hard-coded with atom names and order. POPC there still has a 5-bead oleoyl tail, while the current version of martini now uses a four bead tail. That probably explains the mismatch and the resulting index error. You can change the tail bonds and bead names in line 91 of the script to fix this, replacing:
elif lipid_type == "POPC": bond_names = phosphatidylcholine_bond_names + "GL1-C1B GL2-C1A C1A-C2A C2A-C3A C3A-C4A C1B-C2B C2B-D3B D3B-C4B C4B-C5B\n"
with
elif lipid_type == "POPC": bond_names = phosphatidylcholine_bond_names + "GL1-C1B GL2-C1A C1A-D2A D2A-C3A C3A-C4A C1B-C2B C2B-C3B C3B-C4B\n"
Hope it helps...
In the script, the lipids are hard-coded with atom names and order. POPC there still has a 5-bead oleoyl tail, while the current version of martini now uses a four bead tail. That probably explains the mismatch and the resulting index error. You can change the tail bonds and bead names in line 91 of the script to fix this, replacing:
elif lipid_type == "POPC": bond_names = phosphatidylcholine_bond_names + "GL1-C1B GL2-C1A C1A-C2A C2A-C3A C3A-C4A C1B-C2B C2B-D3B D3B-C4B C4B-C5B\n"
with
elif lipid_type == "POPC": bond_names = phosphatidylcholine_bond_names + "GL1-C1B GL2-C1A C1A-D2A D2A-C3A C3A-C4A C1B-C2B C2B-C3B C3B-C4B\n"
Hope it helps...
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