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martinize: disulfides and output as gro issues
- johnd
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8 years 1 month ago #5449
by johnd
martinize: disulfides and output as gro issues was created by johnd
Hello,
I am coarse-graining a protein and I am having a few issues.
For reference, the protein is 3RFI on rscb, and it has 3 disulfide linkages. The pdb is missing some sections, but these were rebuilt using modeller. I am using gromacs 5.0.4. I used H++ to protonate my protein at pH = 4.5.
The 3 linkages are between cysteine's 11 & 104, 36 & 76, and 42 & 73 in the original pdb. I removed excess residues (added due to the E. coli expression system), so the cys are in different places (6, 31, 37, 68, 71, & 99), and I renumbered the file. The reason I did it this way is because the itp file later is written based on the current file.
Then I cg'ed the structure
I have two issues starting here:
1 - Afterwards martinize leaves a note "Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol", but when I check the protein's itp file, there is nothing in either the bonds section or constraints section that implies the disulfide bonds were created.
Could someone clarify whether I am missing something, or if these bonds were indeed not created. Can I simply add in a 0.24000 nm contraint between appropriate cysteine sidechains?
2 - The martinize script doesn't output in the proper gro format. I have also tried to use pdb2gmx to convert the pdb to a gro first, but then martinize again reformats the file to something unreadable by gromacs. Any idea why this is happening? I am 100% sure I have used this script before and it worked for me then. To be safe I downloaded a new copy of martinize and the issue persisted. I'm using python 2.7.9.
Steps exactly as they were done:
gmx pdb2gmx -f 3rfi_4.5.pdb -o 3rfi_4.5.gro -water none -ignh
Forcefield was amber99sbnmr1-ildn
gmx editconf -f 3rfi_4.5.gro -o 3rfi_4.5.gro -resnr 1
./martinize.py -f 3rfi_4.5.gro -x 3rfi_4.5_cg.gro -dssp /usr/bin/dssp -o topol.top -cys 6,99 -cys 31,71 -cys 37,68
Please see files in dropbox for reference: www.dropbox.com/sh/ckmhc90p25wiu5w/AAAXY...qE2b8CdxQHGV8Fa?dl=0
Any and all help is much appreciated!
Cheers,
John
I am coarse-graining a protein and I am having a few issues.
For reference, the protein is 3RFI on rscb, and it has 3 disulfide linkages. The pdb is missing some sections, but these were rebuilt using modeller. I am using gromacs 5.0.4. I used H++ to protonate my protein at pH = 4.5.
The 3 linkages are between cysteine's 11 & 104, 36 & 76, and 42 & 73 in the original pdb. I removed excess residues (added due to the E. coli expression system), so the cys are in different places (6, 31, 37, 68, 71, & 99), and I renumbered the file. The reason I did it this way is because the itp file later is written based on the current file.
Then I cg'ed the structure
I have two issues starting here:
1 - Afterwards martinize leaves a note "Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol", but when I check the protein's itp file, there is nothing in either the bonds section or constraints section that implies the disulfide bonds were created.
Could someone clarify whether I am missing something, or if these bonds were indeed not created. Can I simply add in a 0.24000 nm contraint between appropriate cysteine sidechains?
2 - The martinize script doesn't output in the proper gro format. I have also tried to use pdb2gmx to convert the pdb to a gro first, but then martinize again reformats the file to something unreadable by gromacs. Any idea why this is happening? I am 100% sure I have used this script before and it worked for me then. To be safe I downloaded a new copy of martinize and the issue persisted. I'm using python 2.7.9.
Steps exactly as they were done:
gmx pdb2gmx -f 3rfi_4.5.pdb -o 3rfi_4.5.gro -water none -ignh
Forcefield was amber99sbnmr1-ildn
gmx editconf -f 3rfi_4.5.gro -o 3rfi_4.5.gro -resnr 1
./martinize.py -f 3rfi_4.5.gro -x 3rfi_4.5_cg.gro -dssp /usr/bin/dssp -o topol.top -cys 6,99 -cys 31,71 -cys 37,68
Please see files in dropbox for reference: www.dropbox.com/sh/ckmhc90p25wiu5w/AAAXY...qE2b8CdxQHGV8Fa?dl=0
Any and all help is much appreciated!
Cheers,
John
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- djurre
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8 years 1 month ago #5453
by djurre
Replied by djurre on topic martinize: disulfides and output as gro issues
Hi John,
You could indeed just add the the constraints as you suggest. However, martinize.py also recognizes the CYS bonds by itself if you set "-cys auto". The syntax as you used should also work, but I can confirm it doesn't. I'll look into that a bit more.
This is a filenaming problem: martinize.py outputs structures in pdb format, but you are telling it to name it "3rfi_4.5_cg.gro". It is not smart in the sense that it doesn't add the right extension. Simple change the filename to <something>.pdb, and gromacs recognizes it.
johnd wrote:
1 - Afterwards martinize leaves a note "Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol", but when I check the protein's itp file, there is nothing in either the bonds section or constraints section that implies the disulfide bonds were created.
Could someone clarify whether I am missing something, or if these bonds were indeed not created. Can I simply add in a 0.24000 nm contraint between appropriate cysteine sidechains?
You could indeed just add the the constraints as you suggest. However, martinize.py also recognizes the CYS bonds by itself if you set "-cys auto". The syntax as you used should also work, but I can confirm it doesn't. I'll look into that a bit more.
johnd wrote: 2 - The martinize script doesn't output in the proper gro format. I have also tried to use pdb2gmx to convert the pdb to a gro first, but then martinize again reformats the file to something unreadable by gromacs. Any idea why this is happening? I am 100% sure I have used this script before and it worked for me then. To be safe I downloaded a new copy of martinize and the issue persisted. I'm using python 2.7.9.
This is a filenaming problem: martinize.py outputs structures in pdb format, but you are telling it to name it "3rfi_4.5_cg.gro". It is not smart in the sense that it doesn't add the right extension. Simple change the filename to <something>.pdb, and gromacs recognizes it.
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- djurre
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8 years 1 month ago - 8 years 1 month ago #5454
by djurre
Replied by djurre on topic martinize: disulfides and output as gro issues
The problem with the ss-bridges is due to an inconsistency in how empty chain identifiers are handle internally. I've logged an issue here:
github.com/cgmartini/martinize.py/issues/7
and try to fix it for a future release.
In the mean time the solution I gave in the previous post works or you can explicitly specify an "empty" chain:
github.com/cgmartini/martinize.py/issues/7
and try to fix it for a future release.
In the mean time the solution I gave in the previous post works or you can explicitly specify an "empty" chain:
-cys " /CYS/15, /CYS/48"
Last edit: 8 years 1 month ago by djurre.
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- johnd
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8 years 1 month ago #5456
by johnd
Replied by johnd on topic martinize: disulfides and output as gro issues
Hi Djurre,
Thank you very much for your help! I have tried the -cys auto option like you said and that worked for me perfectly.
In the meantime I had also figured out my issues with the martinize output format. I was always trying to use pdb2gmx to change from pdb to gro, but now I realized editconf is a much better choice (and simpler).
delete extra residues
editconf > renumber pdb
martinize > output to pdb
editconf > convert pdb to gro
Thanks again,
John
Thank you very much for your help! I have tried the -cys auto option like you said and that worked for me perfectly.
In the meantime I had also figured out my issues with the martinize output format. I was always trying to use pdb2gmx to change from pdb to gro, but now I realized editconf is a much better choice (and simpler).
delete extra residues
editconf > renumber pdb
martinize > output to pdb
editconf > convert pdb to gro
Thanks again,
John
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