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martinize.py bug
- Rajat Desikan
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9 years 8 months ago - 9 years 8 months ago #4020
by Rajat Desikan
martinize.py bug was created by Rajat Desikan
Hi All,
I tried to martinize a protein complex with 7 chains in it (chains A-G). The last seven residues of chain G are missing in the .itp file, i.e., Protein_G.itp, whereas the rest (Protein_A.itp-Protein_F.itp) have all the residues. I checked my dssp file and my input coordinate file (which I have used for AA simulations as well). They seem to be fine. Can anyone help me out with this?
Thanks,
I tried to martinize a protein complex with 7 chains in it (chains A-G). The last seven residues of chain G are missing in the .itp file, i.e., Protein_G.itp, whereas the rest (Protein_A.itp-Protein_F.itp) have all the residues. I checked my dssp file and my input coordinate file (which I have used for AA simulations as well). They seem to be fine. Can anyone help me out with this?
Thanks,
Last edit: 9 years 8 months ago by Rajat Desikan.
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9 years 8 months ago #4025
by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py bug
Hi, any suggestions will be appreciated. Thanks. Has anyone come across a similar problem?
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- djurre
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9 years 8 months ago #4026
by djurre
Replied by djurre on topic martinize.py bug
Hi,
I don't remember exactly but there is/was a problem with do_dssp and multiple chains. The string of SS characters is supposed to be splitted by equals signs (=), but this was in some versions frameshifted by one amino acid. Could that be the problem?
In that case switching to a newer gromacs (do_dssp) or calling dssp directly from martinize.py (e.g.: -dssp /usr/bin/dssp) should fix the problem.
I don't remember exactly but there is/was a problem with do_dssp and multiple chains. The string of SS characters is supposed to be splitted by equals signs (=), but this was in some versions frameshifted by one amino acid. Could that be the problem?
In that case switching to a newer gromacs (do_dssp) or calling dssp directly from martinize.py (e.g.: -dssp /usr/bin/dssp) should fix the problem.
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9 years 8 months ago #4027
by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py bug
Hi Djurre,
Neither strategies worked. I am using gromacs 4.6.4, but I am not sure what do_dssp has got to do with martinize.py
I passed the dssp executable (various versions, new to old) directly to martinize.py, as well as passed the .dssp files directly. Nothing works. The last 7 residues of the 7th chain remain missing!
Interestingly, though the chains are supposed to be identical, the force-field parameters (equilibrium distances for bonds and angles) in the .itp files for the individual chains (say A.itp versus D.itp) are slightly different. Why is that? This didn't happen for another multi-chain protein that I ran Martini simulations with.
Neither strategies worked. I am using gromacs 4.6.4, but I am not sure what do_dssp has got to do with martinize.py
I passed the dssp executable (various versions, new to old) directly to martinize.py, as well as passed the .dssp files directly. Nothing works. The last 7 residues of the 7th chain remain missing!
Interestingly, though the chains are supposed to be identical, the force-field parameters (equilibrium distances for bonds and angles) in the .itp files for the individual chains (say A.itp versus D.itp) are slightly different. Why is that? This didn't happen for another multi-chain protein that I ran Martini simulations with.
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9 years 8 months ago #4028
by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py bug
Update: I tried with an earlier version of martinize.py (Aug 13) that had successfully worked with another protein. I still have the same problem of missing residues.
I am willing to share my files with someone if necessary. I think that this is may be a bug with martinize.py
Thank you.
I am willing to share my files with someone if necessary. I think that this is may be a bug with martinize.py
Thank you.
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9 years 8 months ago #4029
by xavier
Replied by xavier on topic martinize.py bug
Yes I believe this is a bug. I also believe we have had that one already. But I can't remember what the problem was.
It might have been the atom name of the termini in the pdb file that did not match the ones defined in the martinize.
It might have been the atom name of the termini in the pdb file that did not match the ones defined in the martinize.
Rajat Desikan wrote: Update: I tried with an earlier version of martinize.py (Aug 13) that had successfully worked with another protein. I still have the same problem of missing residues.
I am willing to share my files with someone if necessary. I think that this is may be a bug with martinize.py
Thank you.
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9 years 8 months ago #4030
by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py bug
Hi Xavier,
The other chains have termini atoms too, right? The .itp files are just fine for those.
Is there a solution for this? Do you have a corrected version of martinize.py?
Thanks,
The other chains have termini atoms too, right? The .itp files are just fine for those.
Is there a solution for this? Do you have a corrected version of martinize.py?
Thanks,
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9 years 8 months ago #4031
by djurre
Replied by djurre on topic martinize.py bug
Can I find the pdb file somewhere so I can have a look what is going wrong? I than might be able to fix martinize.py
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9 years 8 months ago #4032
by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py bug
Hi Djurre,
It is a modified version of a PDB file with reconstructed residues. Can I mail you the .pdb and any other files that you may require?
Thanks,
It is a modified version of a PDB file with reconstructed residues. Can I mail you the .pdb and any other files that you may require?
Thanks,
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9 years 8 months ago #4034
by djurre
Replied by djurre on topic martinize.py bug
It is as Xavier suggested: the terminal oxigens in your pdb do not have the correct names. They are called 'OC1' and 'OC2' instead of 'O' and 'OXT'. Correcting that in your pdb fixes the 'bug'.
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9 years 8 months ago #4035
by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py bug
Thank you Djurre, Xavier. That worked wonderfully!!
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9 years 8 months ago #4036
by xavier
Replied by xavier on topic martinize.py bug
Beautiful!
I love when things get fixed.
Could we get this on the list or the next martinize version?
Tks
I love when things get fixed.
Could we get this on the list or the next martinize version?
Tks
Rajat Desikan wrote: Thank you Djurre, Xavier. That worked wonderfully!!
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9 years 8 months ago #4037
by djurre
Replied by djurre on topic martinize.py bug
It's not a martinize.py bug. Names of the terminal oxigens should be correctly named ('O' and 'OXT').
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9 years 8 months ago #4038
by Rajat Desikan
Replied by Rajat Desikan on topic martinize.py bug
I had processed the .pdb with pdb2gmx (amber99sb-ildn ff), so I assumed that the termini were properly capped!
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9 years 8 months ago #4040
by xavier
Replied by xavier on topic martinize.py bug
I guess martinize could be improved by detecting these termini names …
Rajat Desikan wrote: I had processed the .pdb with pdb2gmx (amber99sb-ildn ff), so I assumed that the termini were properly capped!
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