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Atomistic collagen to CG issues
- acnash
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7 years 5 months ago #6310
by acnash
Atomistic collagen to CG issues was created by acnash
HI all,
I have an all-atom collagen structured derived from a full collagen protein MD simulation. Inside the pdb, the one collagen protein is made from three collagen polypeptide chains, thus:
A....
TER
B....
TER
C....
END
Also, I have hydroxylysine, which I encoded for by replicating the lysine entry in the script and then modifying the polarity accordingly.
When I run this through the latest copy of martinize, (with or without the -collagen parameter), I end up with only part of the protein, and not even multiple .itp files that a reported by the output. Any thoughts on what might be causing this? Thanks.
INFO Input structure is a PDB file.
INFO Found 35 chains:
INFO 1: (Protein), 1350 atoms in 104 residues.
INFO 2: (Unknown), 17 atoms in 1 residues.
INFO 3: (Protein), 10315 atoms in 842 residues.
INFO 4: (Unknown), 17 atoms in 1 residues.
INFO 5: (Protein), 1268 atoms in 99 residues.
INFO 6: (Unknown), 17 atoms in 1 residues.
INFO 7: (Protein), 925 atoms in 73 residues.
INFO 8: (Unknown), 17 atoms in 1 residues.
INFO 9: (Protein), 494 atoms in 35 residues.
INFO 10: (Unknown), 17 atoms in 1 residues.
INFO 11: (Protein), 4104 atoms in 329 residues.
INFO 12: (Unknown), 17 atoms in 1 residues.
INFO 13: (Protein), 784 atoms in 63 residues.
INFO 14: (Unknown), 17 atoms in 1 residues.
INFO 15: (Protein), 4510 atoms in 367 residues.
INFO 16: (Unknown), 17 atoms in 1 residues.
INFO 17: (Protein), 268 atoms in 21 residues.
INFO 18: (Unknown), 17 atoms in 1 residues.
INFO 19: (Protein), 97 atoms in 8 residues.
INFO 20: (Unknown), 17 atoms in 1 residues.
INFO 21: (Protein), 642 atoms in 49 residues.
INFO 22: (Unknown), 17 atoms in 1 residues.
INFO 23: (Protein), 141 atoms in 11 residues.
INFO 24: (Unknown), 34 atoms in 2 residues.
INFO 25: (Protein), 365 atoms in 31 residues.
INFO 26: (Unknown), 17 atoms in 1 residues.
INFO 27: (Protein), 178 atoms in 14 residues.
INFO 28: (Unknown), 17 atoms in 1 residues.
INFO 29: (Protein), 1786 atoms in 138 residues.
INFO 30: (Unknown), 17 atoms in 1 residues.
INFO 31: (Protein), 10315 atoms in 842 residues.
INFO 32: (Unknown), 17 atoms in 1 residues.
INFO 33: (Protein), 1268 atoms in 99 residues.
INFO 34: (Unknown), 17 atoms in 1 residues.
INFO 35: (Protein), 127 atoms in 8 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 2 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Total size of the system: 3133 residues.
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Written 16 ITP files
INFO Output contains 18 molecules:
INFO 1-> Protein (chain )
INFO 2-> Protein (chain )
INFO 3-> Protein (chain )
INFO 4-> Protein (chain )
INFO 5-> Protein (chain )
INFO 6-> Protein (chain )
INFO 7-> Protein (chain )
INFO 8-> Protein (chain )
INFO 9-> Protein (chain )
INFO 10-> Protein (chain )
INFO 11-> Protein (chain )
INFO 12-> Protein (chain )
INFO 13-> Protein (chain )
INFO 14-> Protein (chain )
INFO 15-> Protein (chain )
INFO 16-> Protein (chain )
INFO 17-> Protein (chain )
INFO 18-> Protein (chain )
INFO Written topology files
INFO Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.
I have an all-atom collagen structured derived from a full collagen protein MD simulation. Inside the pdb, the one collagen protein is made from three collagen polypeptide chains, thus:
A....
TER
B....
TER
C....
END
Also, I have hydroxylysine, which I encoded for by replicating the lysine entry in the script and then modifying the polarity accordingly.
When I run this through the latest copy of martinize, (with or without the -collagen parameter), I end up with only part of the protein, and not even multiple .itp files that a reported by the output. Any thoughts on what might be causing this? Thanks.
INFO Input structure is a PDB file.
INFO Found 35 chains:
INFO 1: (Protein), 1350 atoms in 104 residues.
INFO 2: (Unknown), 17 atoms in 1 residues.
INFO 3: (Protein), 10315 atoms in 842 residues.
INFO 4: (Unknown), 17 atoms in 1 residues.
INFO 5: (Protein), 1268 atoms in 99 residues.
INFO 6: (Unknown), 17 atoms in 1 residues.
INFO 7: (Protein), 925 atoms in 73 residues.
INFO 8: (Unknown), 17 atoms in 1 residues.
INFO 9: (Protein), 494 atoms in 35 residues.
INFO 10: (Unknown), 17 atoms in 1 residues.
INFO 11: (Protein), 4104 atoms in 329 residues.
INFO 12: (Unknown), 17 atoms in 1 residues.
INFO 13: (Protein), 784 atoms in 63 residues.
INFO 14: (Unknown), 17 atoms in 1 residues.
INFO 15: (Protein), 4510 atoms in 367 residues.
INFO 16: (Unknown), 17 atoms in 1 residues.
INFO 17: (Protein), 268 atoms in 21 residues.
INFO 18: (Unknown), 17 atoms in 1 residues.
INFO 19: (Protein), 97 atoms in 8 residues.
INFO 20: (Unknown), 17 atoms in 1 residues.
INFO 21: (Protein), 642 atoms in 49 residues.
INFO 22: (Unknown), 17 atoms in 1 residues.
INFO 23: (Protein), 141 atoms in 11 residues.
INFO 24: (Unknown), 34 atoms in 2 residues.
INFO 25: (Protein), 365 atoms in 31 residues.
INFO 26: (Unknown), 17 atoms in 1 residues.
INFO 27: (Protein), 178 atoms in 14 residues.
INFO 28: (Unknown), 17 atoms in 1 residues.
INFO 29: (Protein), 1786 atoms in 138 residues.
INFO 30: (Unknown), 17 atoms in 1 residues.
INFO 31: (Protein), 10315 atoms in 842 residues.
INFO 32: (Unknown), 17 atoms in 1 residues.
INFO 33: (Protein), 1268 atoms in 99 residues.
INFO 34: (Unknown), 17 atoms in 1 residues.
INFO 35: (Protein), 127 atoms in 8 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 2 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Total size of the system: 3133 residues.
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Written 16 ITP files
INFO Output contains 18 molecules:
INFO 1-> Protein (chain )
INFO 2-> Protein (chain )
INFO 3-> Protein (chain )
INFO 4-> Protein (chain )
INFO 5-> Protein (chain )
INFO 6-> Protein (chain )
INFO 7-> Protein (chain )
INFO 8-> Protein (chain )
INFO 9-> Protein (chain )
INFO 10-> Protein (chain )
INFO 11-> Protein (chain )
INFO 12-> Protein (chain )
INFO 13-> Protein (chain )
INFO 14-> Protein (chain )
INFO 15-> Protein (chain )
INFO 16-> Protein (chain )
INFO 17-> Protein (chain )
INFO 18-> Protein (chain )
INFO Written topology files
INFO Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.
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- acnash
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- Posts: 24
7 years 5 months ago #6311
by acnash
Replied by acnash on topic Atomistic collagen to CG issues
Sorry - this is a duplicate thread. If an admin could remove this thread I would be grateful. Thanks.
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