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martinize2 error with termini
- Spinetti
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2 years 10 months ago #8988
by Spinetti
martinize2 error with termini was created by Spinetti
Hi everyone,
I want to use martini 3 on a protein dimer that I previously simulated in an atomistic setting and with martini 2. Trying to martinize the structure using martinize2, I did:
martinize2 -f npt-protein.gro -o LD-dimer.top -x LD-dimerCG.pdb -p backbone -ff martini3001 -dssp /usr/local/bin/mkdssp
But I get the following error:
ERROR - general - Modification N-ter doesn't fit on Block PRO
How do you suggest to avoid this error, that never came out using the old martinize?
Thank you very much for your help
Elena
I want to use martini 3 on a protein dimer that I previously simulated in an atomistic setting and with martini 2. Trying to martinize the structure using martinize2, I did:
martinize2 -f npt-protein.gro -o LD-dimer.top -x LD-dimerCG.pdb -p backbone -ff martini3001 -dssp /usr/local/bin/mkdssp
But I get the following error:
ERROR - general - Modification N-ter doesn't fit on Block PRO
How do you suggest to avoid this error, that never came out using the old martinize?
Thank you very much for your help
Elena
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- peterkroon
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2 years 10 months ago #8990
by peterkroon
Replied by peterkroon on topic martinize2 error with termini
Hi Elena,
what version of martinize2 are you using (martinize2 -version)?
what version of martinize2 are you using (martinize2 -version)?
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2 years 10 months ago #8991
by Spinetti
Replied by Spinetti on topic martinize2 error with termini
Hi peterkroon,
thank you for your answer.
I have the following:
martinize2 -V
martinize with vermouth 0.7.1
thank you for your answer.
I have the following:
martinize2 -V
martinize with vermouth 0.7.1
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2 years 10 months ago #9000
by peterkroon
Replied by peterkroon on topic martinize2 error with termini
Sorry for the late reply.
I thought we had fixed that issue, but you're running the latest version. I'll dig into it.
As a workaround, add -nter none and patch the n-teminus by hand in the output itp.
I thought we had fixed that issue, but you're running the latest version. I'll dig into it.
As a workaround, add -nter none and patch the n-teminus by hand in the output itp.
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2 years 10 months ago #9003
by Spinetti
Replied by Spinetti on topic martinize2 error with termini
No problem, thank you for the answer.
Unfortunately, I tried adding '-nter none' but martinize2 gets stuck with this message:
INFO - general - Applying modification none to residue -PRO1
Unfortunately, I tried adding '-nter none' but martinize2 gets stuck with this message:
INFO - general - Applying modification none to residue -PRO1
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2 years 10 months ago #9004
by Spinetti
Replied by Spinetti on topic martinize2 error with termini
No problem, thank you for the answer.
Unfortunately, I tried adding '-nter none' but martinize2 gets stuck with this message:
INFO - general - Applying modification none to residue -PRO1
Unfortunately, I tried adding '-nter none' but martinize2 gets stuck with this message:
INFO - general - Applying modification none to residue -PRO1
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- peterkroon
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2 years 10 months ago #9009
by peterkroon
Replied by peterkroon on topic martinize2 error with termini
Curious. When you say 'stuck', how long are we talking about? Could you run with -vv?
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2 years 10 months ago #9010
by Spinetti
Replied by Spinetti on topic martinize2 error with termini
It is frozen for a long time, more than half an hour, so I killed it. I am trying to tun -vv, I will let you know.
Also, could the problem be because I am modeling a dimer? Maybe some issue with the numbering.
But anyway, I had exactly the same before and martini 2 never complained.
Also, could the problem be because I am modeling a dimer? Maybe some issue with the numbering.
But anyway, I had exactly the same before and martini 2 never complained.
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2 years 10 months ago #9011
by peterkroon
Replied by peterkroon on topic martinize2 error with termini
There is no problem with dimers. It could be that your structure is not great, and that there are erroneous bonds between the dimers based on the distances. -vv will/should tell you.
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2 years 10 months ago - 2 years 10 months ago #9013
by Spinetti
Replied by Spinetti on topic martinize2 error with termini
The messages I get are (for all the residues, I report only some examples):
Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm27
...
DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1-PRO1:CAY and 2-PRO1:HY1 based on distance.
....
WARNING - general - vermouth.processors.make_bonds - Can't add bonds based on atom names for residue -GLU2 because 'Residue has multiple atoms with atom name N'. Falling back to distance criteria.
...
DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 7851-ASP161:CA and 7853-ASP161:CB based on distance.
...
INFO - general - vermouth.processors.make_bonds - 1 molecules after guessing bonds
DEBUG - step - vermouth - Annotating required mutations and modifications.
DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating PRO1 with modification none
DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating PRO340 with modification none
INFO - step - vermouth - Repairing the graph.
DEBUG - step - vermouth.processors.repair_graph - Making reference graph
INFO - general - vermouth.processors.repair_graph - Applying modification none to residue -PRO1
DEBUG - step - vermouth.processors.repair_graph - Matching residue -PRO1 to its reference
And after the last message, it is stuck.
Level 5 - inconsistent-data - vermouth.map_input - Can't find block VAL for FF charmm27
...
DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1-PRO1:CAY and 2-PRO1:HY1 based on distance.
....
WARNING - general - vermouth.processors.make_bonds - Can't add bonds based on atom names for residue -GLU2 because 'Residue has multiple atoms with atom name N'. Falling back to distance criteria.
...
DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 7851-ASP161:CA and 7853-ASP161:CB based on distance.
...
INFO - general - vermouth.processors.make_bonds - 1 molecules after guessing bonds
DEBUG - step - vermouth - Annotating required mutations and modifications.
DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating PRO1 with modification none
DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating PRO340 with modification none
INFO - step - vermouth - Repairing the graph.
DEBUG - step - vermouth.processors.repair_graph - Making reference graph
INFO - general - vermouth.processors.repair_graph - Applying modification none to residue -PRO1
DEBUG - step - vermouth.processors.repair_graph - Matching residue -PRO1 to its reference
And after the last message, it is stuck.
Last edit: 2 years 10 months ago by Spinetti. Reason: errors
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2 years 10 months ago #9015
by peterkroon
Replied by peterkroon on topic martinize2 error with termini
Thanks.
This:
> WARNING - general - vermouth.processors.make_bonds - Can't add bonds based on atom names for residue -GLU2 because 'Residue has multiple atoms with atom name N'. Falling back to distance criteria.
is a really bad sign. Check your input structure, and in particular GLU2. You have a dimer right? Are there either chain IDs, or a TER record in between them? Or are the residue numbers unique?
> INFO - general - vermouth.processors.make_bonds - 1 molecules after guessing bonds
Indicates something went wrong with your dimer...
This:
> WARNING - general - vermouth.processors.make_bonds - Can't add bonds based on atom names for residue -GLU2 because 'Residue has multiple atoms with atom name N'. Falling back to distance criteria.
is a really bad sign. Check your input structure, and in particular GLU2. You have a dimer right? Are there either chain IDs, or a TER record in between them? Or are the residue numbers unique?
> INFO - general - vermouth.processors.make_bonds - 1 molecules after guessing bonds
Indicates something went wrong with your dimer...
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2 years 10 months ago #9016
by Spinetti
Replied by Spinetti on topic martinize2 error with termini
Thank you very much,
I was using a gro file without unique identifiers, so I converted it in pdb format, with different chain identifiers for the two monomers and now it can recognize the 2 separate molecules.
Unfortunately, I am still not able to produce the martini structure, as I get this error:
Error trying to load file "/Users/elenaspinetti/Documents/PhD-projects/IRE1/1-data/11-martini3/LD/1-system-setup/dssp_in_oxywrk9_.pdb"
Expected record CRYST1 but found ATOM
even though my pdb header is:
CRYST1 149.964 149.964 149.964 90.00 90.00 90.00 P 1 1
ATOM 1 CAY PRO A 1 57.330 50.070 59.450 1.00 0.00 C
ATOM 2 HY1 PRO A 1 56.270 49.740 59.330 1.00 0.00 H
ATOM 3 HY2 PRO A 1 57.740 49.710 60.420 1.00 0.00 H
Maybe is a problem with my dssp installation... What do you think?
I was using a gro file without unique identifiers, so I converted it in pdb format, with different chain identifiers for the two monomers and now it can recognize the 2 separate molecules.
Unfortunately, I am still not able to produce the martini structure, as I get this error:
Error trying to load file "/Users/elenaspinetti/Documents/PhD-projects/IRE1/1-data/11-martini3/LD/1-system-setup/dssp_in_oxywrk9_.pdb"
Expected record CRYST1 but found ATOM
even though my pdb header is:
CRYST1 149.964 149.964 149.964 90.00 90.00 90.00 P 1 1
ATOM 1 CAY PRO A 1 57.330 50.070 59.450 1.00 0.00 C
ATOM 2 HY1 PRO A 1 56.270 49.740 59.330 1.00 0.00 H
ATOM 3 HY2 PRO A 1 57.740 49.710 60.420 1.00 0.00 H
Maybe is a problem with my dssp installation... What do you think?
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2 years 10 months ago #9022
by peterkroon
Replied by peterkroon on topic martinize2 error with termini
Indeed DSSP is to blame (well, kind of). See
github.com/marrink-lab/vermouth-martinize/issues/364
Short summary, you need dssp 3, and I guess you have version 4.
Short summary, you need dssp 3, and I guess you have version 4.
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2 years 9 months ago #9074
by Spinetti
Replied by Spinetti on topic martinize2 error with termini
Thank you very much again for your answers.
I managed to obtain the model of my protein dimer.
However, it is unclear to me what "-nter none -cter none" does to modify the topology. What I get in the itp file termini is:
1609 SP2a 680 PRO BB 1609 0.0
1610 SC3 680 PRO SC1 1610 0.0
Does it leave the termini unchanged?
I managed to obtain the model of my protein dimer.
However, it is unclear to me what "-nter none -cter none" does to modify the topology. What I get in the itp file termini is:
1609 SP2a 680 PRO BB 1609 0.0
1610 SC3 680 PRO SC1 1610 0.0
Does it leave the termini unchanged?
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2 years 9 months ago #9075
by peterkroon
Replied by peterkroon on topic martinize2 error with termini
Correct. You end up with unpatched (i.e. uncharged) termini.
By now this should be fixed in the master branch (per github.com/marrink-lab/vermouth-martiniz...9be940b1b6043ff4d2d5 ). If you're feeling adventurous you can give installing the development version a try.
By now this should be fixed in the master branch (per github.com/marrink-lab/vermouth-martiniz...9be940b1b6043ff4d2d5 ). If you're feeling adventurous you can give installing the development version a try.
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