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Missing Atoms in Separated DNA/Protein Complex
- jonasori
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7 years 10 months ago #5712
by jonasori
Missing Atoms in Separated DNA/Protein Complex was created by jonasori
Hello all,
I've worked through the DNA/protein tutorial (which was very nice), and am currently trying to follow the same steps with a different file (I arbitrarily chose 5J3E ).
When I go to break it into parts, I remove all the comments and such above the coordinate data, then separate the protein by grep'ing out everything that is not DNA (i.e. grep -v 'DG\|DC\|DA\|DT' complex.pdb > protein.pdb), and using the same approach (only without the -v) to get the DNA.
However, visual inspection in VMD shows that after doing this, the DNA strands separate and are each broken into three distinct chunks. That seems a little worrisome, but has not yet produced any fatal errors.
However, I am getting a fatal error when I try to run the isolated protein, giving me the response:
INFO MARTINIZE, script version 2.4
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The elnedyn22 forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 2 chains:
INFO 1: A (Protein), 1372 atoms in 172 residues.
INFO 2: B (Protein), 1356 atoms in 171 residues.
INFO Total size of the system: 343 residues.
INFO Writing coarse grained structure.
ERROR Too many atoms missing from residue LYS 69(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 85(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 142(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 152(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 170(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 200(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 222(ch:A):
ERROR
ERROR Unable to generate coarse grained structure due to missing atoms.
I'm not sure where the missing atoms have gone (obviously). Does anyone know what's going on here? I'm guessing that my error was somewhere in my atom selection, when I broke the molecules apart.
Any help is greatly appreciated, as always.
Thanks,
Jonas
I've worked through the DNA/protein tutorial (which was very nice), and am currently trying to follow the same steps with a different file (I arbitrarily chose 5J3E ).
When I go to break it into parts, I remove all the comments and such above the coordinate data, then separate the protein by grep'ing out everything that is not DNA (i.e. grep -v 'DG\|DC\|DA\|DT' complex.pdb > protein.pdb), and using the same approach (only without the -v) to get the DNA.
However, visual inspection in VMD shows that after doing this, the DNA strands separate and are each broken into three distinct chunks. That seems a little worrisome, but has not yet produced any fatal errors.
However, I am getting a fatal error when I try to run the isolated protein, giving me the response:
INFO MARTINIZE, script version 2.4
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The elnedyn22 forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 2 chains:
INFO 1: A (Protein), 1372 atoms in 172 residues.
INFO 2: B (Protein), 1356 atoms in 171 residues.
INFO Total size of the system: 343 residues.
INFO Writing coarse grained structure.
ERROR Too many atoms missing from residue LYS 69(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 85(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 142(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 152(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 170(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 200(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 222(ch:A):
ERROR
ERROR Unable to generate coarse grained structure due to missing atoms.
I'm not sure where the missing atoms have gone (obviously). Does anyone know what's going on here? I'm guessing that my error was somewhere in my atom selection, when I broke the molecules apart.
Any help is greatly appreciated, as always.
Thanks,
Jonas
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- peterkroon
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7 years 10 months ago #5713
by peterkroon
Replied by peterkroon on topic Missing Atoms in Separated DNA/Protein Complex
Hi,
my suspicion is that your crystal structure is missing atoms. I've been told this is quite common.
Use your favorite software (e.g. PyMol) to complete it.
Peter
my suspicion is that your crystal structure is missing atoms. I've been told this is quite common.
Use your favorite software (e.g. PyMol) to complete it.
Peter
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- jonasori
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7 years 10 months ago - 7 years 5 months ago #5714
by jonasori
Replied by jonasori on topic Missing Atoms in Separated DNA/Protein Complex
Awesome - that totally did the trick. Thanks for the help!
(for future people: I used lorentz.immstr.pasteur.fr/pdb/frozen_submission.php )
Jonas
EDIT: While that website can work, Swiss PDB Viewer is a much better option. It will automatically complete your molecule upon import, and then offers a lot of deeper control over structure than you get with a simple website (obviously). Definitely worth downloading and getting used to.
(for future people: I used lorentz.immstr.pasteur.fr/pdb/frozen_submission.php )
Jonas
EDIT: While that website can work, Swiss PDB Viewer is a much better option. It will automatically complete your molecule upon import, and then offers a lot of deeper control over structure than you get with a simple website (obviously). Definitely worth downloading and getting used to.
Last edit: 7 years 5 months ago by jonasori. Reason: Better option for crystal structure completion
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7 years 10 months ago - 7 years 10 months ago #5715
by jonasori
Replied by jonasori on topic Missing Atoms in Separated DNA/Protein Complex
Actually, while I'm here, I've got another quick question. I've noticed that the file from the PDB is the complex's asymmetric unit, with two double-helices and proteins (screenshot:
drive.google.com/file/d/0B8BjSI3DQR36NmF...bnM/view?usp=sharing
). Intuitively, it seems to me that I should be cutting that down to just the biological assembly instead. What is the normal protocol for this?
Thanks,
Jonas
Thanks,
Jonas
Last edit: 7 years 10 months ago by jonasori.
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- peterkroon
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7 years 10 months ago #5716
by peterkroon
Replied by peterkroon on topic Missing Atoms in Separated DNA/Protein Complex
What do you mean with the "biological assembly"?
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7 years 10 months ago #5717
by jonasori
Replied by jonasori on topic Missing Atoms in Separated DNA/Protein Complex
My bad - I just used the word that they used on the PDB page (
the label on the picture in the center-left
). By biological assembly I mean just the single ds-DNA and the protein, rather than the doubled version.
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7 years 9 months ago #5719
by peterkroon
Replied by peterkroon on topic Missing Atoms in Separated DNA/Protein Complex
It's a very simple question: What do you want to simulate? If the protein exists as a dimer in nature, that may be more realistic than the monomer. Either way, if you simulate the dimer, you also get double the statistics, so it may be worth it either way.
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