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Incorrect number of parameters error
- Hongtham
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8 years 8 months ago - 8 years 8 months ago #4800
by Hongtham
Incorrect number of parameters error was created by Hongtham
Hi all,
I set up simulation with a protein and I useed martinize.py to convert from aa to cg with -cys option to detect the disulfide bond between cystein residues
But when I run simulation, I could not make the .tpr. It returned the error: (Incorrect number of parameters - found 1, expected 2 or 4 for Bond.)
I found that, because the bond parameter for Cystine bridges was different from normal pairs ( I show below, the bolded letters. How can I fix this problem?
Thank you so much.
Hongtham
[ bonds ]
; Backbone bonds
1 5 1 0.35000 1250 ; PHE(C)-GLN(C)
31 33 1 0.35000 1250 ; ASN(T)-TYR(C)
33 37 1 0.35000 1250 ; TYR(C)-ASN(C)
; Links/Cystine bridges
300 340 1 0.24000
452 454 1 0.24000
I set up simulation with a protein and I useed martinize.py to convert from aa to cg with -cys option to detect the disulfide bond between cystein residues
But when I run simulation, I could not make the .tpr. It returned the error: (Incorrect number of parameters - found 1, expected 2 or 4 for Bond.)
I found that, because the bond parameter for Cystine bridges was different from normal pairs ( I show below, the bolded letters. How can I fix this problem?
Thank you so much.
Hongtham
[ bonds ]
; Backbone bonds
1 5 1 0.35000 1250 ; PHE(C)-GLN(C)
31 33 1 0.35000 1250 ; ASN(T)-TYR(C)
33 37 1 0.35000 1250 ; TYR(C)-ASN(C)
; Links/Cystine bridges
300 340 1 0.24000
452 454 1 0.24000
Last edit: 8 years 8 months ago by Hongtham. Reason: mistake information
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- djurre
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8 years 8 months ago #4804
by djurre
Replied by djurre on topic Incorrect number of parameters error
Could it be you are not using the latest (2.4) version of martinize.py? In this version we fixed some issues with the Cys-bridges:
cgmartini.nl/cgmartini/index.php/tools2/...layers/204-martinize
cgmartini.nl/cgmartini/index.php/tools2/...layers/204-martinize
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- Hongtham
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8 years 8 months ago #4806
by Hongtham
Replied by Hongtham on topic Incorrect number of parameters error
Hi,
Thank you for your reply. I used the martinize.py ver 2.4 (the lastest one in the martini website) but I still met this issue.
Best regards,
Hongtham
Thank you for your reply. I used the martinize.py ver 2.4 (the lastest one in the martini website) but I still met this issue.
Best regards,
Hongtham
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- djurre
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8 years 8 months ago #4813
by djurre
Replied by djurre on topic Incorrect number of parameters error
There was a bug, I had fixed it but it never got published. We now put online a new version of the script where is should be fixed:
cgmartini.nl/cgmartini/index.php/tools2/...layers/204-martinize
cgmartini.nl/cgmartini/index.php/tools2/...layers/204-martinize
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- Hongtham
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8 years 6 months ago #5075
by Hongtham
Replied by Hongtham on topic Incorrect number of parameters error
hi, I have update my protocol with the new one. Thank you so much.
Best regards,
Hongtham
Best regards,
Hongtham
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