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How could I solve constraint(?) problem
- Jinyoung
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3 years 1 month ago #8873
by Jinyoung
How could I solve constraint(?) problem was created by Jinyoung
Hi everyone!
I've tried to practice simulating transmembrane protein-POPC bilayer system.
To build system, I downloaded the topology files and structure files from CHARMM-GUI. But as the system size was smaller than I expected, I removed the solvent in .gro file and re-solvate system as below:
python insane.py -f nopbc_nosolv_system.gro -pbc square -box ${box_x},${box_y},75 -d 0 -salt 0.15 -sol PW -o system_solv_ions.gro
And When I tried to equilibration step after energy minimization step, I encountered the errors as below:
ERROR: Cannot have constraint (1-2) with virtual site (2)
ERROR: Cannot have constraint (5-6) with virtual site (6)
ERROR: Cannot have constraint (34-35) with virtual site (35)
ERROR: Cannot have constraint (42-43) with virtual site (43)
ERROR: Cannot have constraint (61-62) with virtual site (62)
ERROR: Cannot have constraint (66-67) with virtual site (67)
ERROR: Cannot have constraint (74-75) with virtual site (75)
ERROR: Cannot have constraint (83-84) with virtual site (84)
ERROR: Cannot have constraint (87-88) with virtual site (88)
ERROR: Cannot have constraint (91-92) with virtual site (92)
ERROR: Cannot have constraint (97-98) with virtual site (98)
How can I solve this errors? I wonder is there any what I'm missing???
Thank you!
I've tried to practice simulating transmembrane protein-POPC bilayer system.
To build system, I downloaded the topology files and structure files from CHARMM-GUI. But as the system size was smaller than I expected, I removed the solvent in .gro file and re-solvate system as below:
python insane.py -f nopbc_nosolv_system.gro -pbc square -box ${box_x},${box_y},75 -d 0 -salt 0.15 -sol PW -o system_solv_ions.gro
And When I tried to equilibration step after energy minimization step, I encountered the errors as below:
ERROR: Cannot have constraint (1-2) with virtual site (2)
ERROR: Cannot have constraint (5-6) with virtual site (6)
ERROR: Cannot have constraint (34-35) with virtual site (35)
ERROR: Cannot have constraint (42-43) with virtual site (43)
ERROR: Cannot have constraint (61-62) with virtual site (62)
ERROR: Cannot have constraint (66-67) with virtual site (67)
ERROR: Cannot have constraint (74-75) with virtual site (75)
ERROR: Cannot have constraint (83-84) with virtual site (84)
ERROR: Cannot have constraint (87-88) with virtual site (88)
ERROR: Cannot have constraint (91-92) with virtual site (92)
ERROR: Cannot have constraint (97-98) with virtual site (98)
How can I solve this errors? I wonder is there any what I'm missing???
Thank you!
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