normal Issue with martinize.py

  • P_Banerjee
  • P_Banerjee's Avatar Topic Author
  • Offline
  • Junior Boarder
More
5 years 1 month ago #8043 by P_Banerjee
Issue with martinize.py was created by P_Banerjee
Hello Martini community,

On using martinize.py script on the pdb structure of GFP (obtained from rcsb website), I see that the number of beads in the CG pdb file does not match with that in the topology. Anyone knows what could be the reason and how to tackle this?

Thanks.

Best,
Pallavi

Please Log in or Create an account to join the conversation.

More
5 years 1 month ago #8044 by peterkroon
Replied by peterkroon on topic Issue with martinize.py
Hi,

1) Where did you get martinize.py? There's a few versions in circulation
2) how did you invoke martinize.py? Please copy paste the exact command line
3) What was the output of martinize.py? What did it print to the screen?

Peter

Please Log in or Create an account to join the conversation.

More
5 years 1 month ago #8045 by jbarnoud
Replied by jbarnoud on topic Issue with martinize.py
Hi Pallavi,

Can you check that the C-terminus match between the structure and the topology? If they do not, then rename the oxygens of the terminus as O1 and O2; DSSP do not always like the name of these atoms.

Please Log in or Create an account to join the conversation.

  • P_Banerjee
  • P_Banerjee's Avatar Topic Author
  • Offline
  • Junior Boarder
More
5 years 1 month ago #8046 by P_Banerjee
Replied by P_Banerjee on topic Issue with martinize.py
Hi Peter,

I'm using the following martinize script.: www.cgmartini.nl/images/tools/martinize/...ize-2.6/martinize.py
And I'm using pyhton version 2.7.5

I invoked the following command:
./martinize.py -f gfp.pdb -o gfp-cg.top -x gfp-cg.pdb -dssp /usr/bin/dssp -p backbone -ff martini22

Martini spewed out the following message:

INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 21 chains:
INFO 1: (Protein), 323 atoms in 22 residues.
INFO 2: (Unknown), 17 atoms in 1 residues.
INFO 3: (Protein), 595 atoms in 39 residues.
INFO 4: (Unknown), 36 atoms in 1 residues.
INFO 5: (Protein), 146 atoms in 9 residues.
INFO 6: (Unknown), 17 atoms in 1 residues.
INFO 7: (Protein), 56 atoms in 3 residues.
INFO 8: (Unknown), 17 atoms in 1 residues.
INFO 9: (Protein), 914 atoms in 57 residues.
INFO 10: (Unknown), 17 atoms in 1 residues.
INFO 11: (Protein), 137 atoms in 8 residues.
INFO 12: (Unknown), 17 atoms in 1 residues.
INFO 13: (Protein), 347 atoms in 20 residues.
INFO 14: (Unknown), 17 atoms in 1 residues.
INFO 15: (Protein), 152 atoms in 11 residues.
INFO 16: (Unknown), 17 atoms in 1 residues.
INFO 17: (Protein), 250 atoms in 17 residues.
INFO 18: (Unknown), 17 atoms in 1 residues.
INFO 19: (Protein), 268 atoms in 17 residues.
INFO 20: (Unknown), 17 atoms in 1 residues.
INFO 21: (Protein), 197 atoms in 13 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 Total size of the system: 216 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 Written 11 ITP files
INFO Output contains 11 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 Written topology files
INFO Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.

Do let me know if I should send some files. Thanks a lot!

Please Log in or Create an account to join the conversation.

  • P_Banerjee
  • P_Banerjee's Avatar Topic Author
  • Offline
  • Junior Boarder
More
5 years 1 month ago #8047 by P_Banerjee
Replied by P_Banerjee on topic Issue with martinize.py
Hi jbarnoud,

The C-terminus oxygens in my atomistic pdb are: O and OXT. Is that a problem?

Thanks.

Please Log in or Create an account to join the conversation.

  • P_Banerjee
  • P_Banerjee's Avatar Topic Author
  • Offline
  • Junior Boarder
More
5 years 1 month ago #8048 by P_Banerjee
Replied by P_Banerjee on topic Issue with martinize.py
Hello,

I managed to fix the issue. Histidine residues in my atomistic pdb were named as HIE, which martizine failed to recognize. On changing their name to HIS, the script worked just fine.

Thanks.

Please Log in or Create an account to join the conversation.

Time to create page: 0.108 seconds