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How to modify disulfide bonds constrain in homology modeling

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How to modify disulfide bonds constrain in homology modeling
#1

Now, I'm using a homology_modeling_with_end_extension.

I want to modify disulf bonds constrain in homology modeling.

I got a homology template files, and got a fixed.grishin files.

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[eunwook@channel template_file]$ ls
1axhA.pdb 1h9hI.pdb 1lu0A.pdb 2jtkA.pdb 2z7fI.pdb 4a94C.pdb
1cr8A.pdb 1h9iI.pdb 1udkA.pdb 2ljsA.pdb 3fjuB.pdb Ia_file.grishin
1fleI.pdb 1hvwA.pdb 1wqcA.pdb 2po8A.pdb 3nggA.pdb Ia_file.hhr

[eunwook@channel homology]$ ls
Ia_file_fixed.grishin README.txt scripts template_file
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Next in minirosetta.linuxgccrelease @comparative_modeling.args this step.

I want to modify disulf constrain between specific residues by using as below

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[eunwook@channel Ia]$ ls
disulf.ini disulf.cst disulf_fa.cst
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But, as you know, constrain was already set by each templates.

How to modify disulf constrain without ERROR?

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core.conformation.util: (0) WARNING: change_cys_state() was called on non-cys residue 15, skipping!
core.conformation.Conformation: (0) Failed to introduce CYD for disulfide (11, 15).
core.conformation.util: (0) WARNING: change_cys_state() was called on non-cys residue 23, skipping!
core.conformation.Conformation: (0) Failed to introduce CYD for disulfide (23, 24).
core.conformation.Conformation: (0) [ERROR] Residue 76 is out of range.
ERROR:: Exit from: src/core/conformation/Conformation.cc line: 1708
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Post Situation: 
Mon, 2013-05-13 04:56
eunwook

The error is that the instructions you have given Rosetta regarding disulfides are not numbered correctly relative to the actual structure - those residue positions aren't cystines in the actual model in two cases, and is just clear off the end of the model in the third (I assume your structure is fewer than 76 residues). What modifications did you make?

Sun, 2013-09-22 14:43
smlewis