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ion-protein complexes in martinize.py
- mferraro
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11 years 3 days ago #1543
by mferraro
ion-protein complexes in martinize.py was created by mferraro
Hi all,
I'm trying to generate a CG description of my protein using martinize.py script. In my pdb file I have two structural SODIUM IONS that are not recognized by the script. I have activated the flag "-hetatm" to retain them but similarly they are not included in topology file. How can I convert the all-atom description in the coarse grained one? Is it necessary to include the coarse grained description of these structural ions to stabilize the CG architecture of the protein?
Any suggestion will be appreciated.
Thanks in advance.
I'm trying to generate a CG description of my protein using martinize.py script. In my pdb file I have two structural SODIUM IONS that are not recognized by the script. I have activated the flag "-hetatm" to retain them but similarly they are not included in topology file. How can I convert the all-atom description in the coarse grained one? Is it necessary to include the coarse grained description of these structural ions to stabilize the CG architecture of the protein?
Any suggestion will be appreciated.
Thanks in advance.
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- djurre
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11 years 2 days ago #1545
by djurre
Replied by djurre on topic ion-protein complexes in martinize.py
The script will indeed not handle the IONs. Since the mapping of the ions is one to one, the position atomistic and coarse-grained will be the same.
However, the model for ions might not be good enough to keep the ions bound in the right position and the protein stable due to that (Atomisticially this is might also be the case?).
If you are using an elastic network, for example Elnedyn, the ternary structure of your protein will be kept stable anyway, with or without the ions. So that would probably solve you problem.
However, the model for ions might not be good enough to keep the ions bound in the right position and the protein stable due to that (Atomisticially this is might also be the case?).
If you are using an elastic network, for example Elnedyn, the ternary structure of your protein will be kept stable anyway, with or without the ions. So that would probably solve you problem.
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- mferraro
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11 years 2 days ago #1547
by mferraro
Replied by mferraro on topic ion-protein complexes in martinize.py
Hi Djurre,
thanks for your precious reply!
thanks for your precious reply!
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- xavier
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10 years 11 months ago #1584
by xavier
I'd like to add that if you like to keep the ion in the protein you could simply place them your self in the CG.pdb/gro file and add bonds to the ligands by hand in the topology file. A regular harmonic bond with a 10000 kJ/mol/nm2 fore constant should be fine.
Just out of curiosity: I am not aware of proteins with structural sodium ions. Are you sure this is the case?
Replied by xavier on topic ion-protein complexes in martinize.py
mferraro wrote: Hi Djurre,
thanks for your precious reply!
I'd like to add that if you like to keep the ion in the protein you could simply place them your self in the CG.pdb/gro file and add bonds to the ligands by hand in the topology file. A regular harmonic bond with a 10000 kJ/mol/nm2 fore constant should be fine.
Just out of curiosity: I am not aware of proteins with structural sodium ions. Are you sure this is the case?
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