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Membrane protein complex
- Rajat Desikan
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12 years 4 months ago #857
by Rajat Desikan
Membrane protein complex was created by Rajat Desikan
Hi
I have a POPC membrane protein complex. Does using the martinize.py in general give the topology file for the whole protein-membrane system or just the protein. And I didn't find a structure for POPC (though I found forcefield parameters). So, how do I go about this? Take the POPE bilayer, replace PE by PC and then equilibrate? Thanks
I have a POPC membrane protein complex. Does using the martinize.py in general give the topology file for the whole protein-membrane system or just the protein. And I didn't find a structure for POPC (though I found forcefield parameters). So, how do I go about this? Take the POPE bilayer, replace PE by PC and then equilibrate? Thanks
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- jantunes
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12 years 4 months ago #858
by jantunes
Replied by jantunes on topic Membrane protein complex
Hey,
Martinize.py just gives the topology for the protein.
Probably that is the best way, like it says in http://md.chem.rug.nl/cgmartini/index.php/tutorial/different-bilayers .
Cumps
Martinize.py just gives the topology for the protein.
Probably that is the best way, like it says in http://md.chem.rug.nl/cgmartini/index.php/tutorial/different-bilayers .
Cumps
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- xavier
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12 years 4 months ago #877
by xavier
Did you sort things out? You could optain aPOPE membrane in the manner you describe indeed and the lipid and protein topologies should be made separately.
Replied by xavier on topic Membrane protein complex
Rajat Desikan wrote: Hi
I have a POPC membrane protein complex. Does using the martinize.py in general give the topology file for the whole protein-membrane system or just the protein. And I didn't find a structure for POPC (though I found forcefield parameters). So, how do I go about this? Take the POPE bilayer, replace PE by PC and then equilibrate? Thanks
Did you sort things out? You could optain aPOPE membrane in the manner you describe indeed and the lipid and protein topologies should be made separately.
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- Rajat Desikan
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12 years 4 months ago #879
by Rajat Desikan
Replied by Rajat Desikan on topic Membrane protein complex
yeah, sort of :)
I managed to obtain a POPC membrane...however, I am yet to energy minimize and equilibrate it...i will keep you posted on the development...thanks a lot :)
I managed to obtain a POPC membrane...however, I am yet to energy minimize and equilibrate it...i will keep you posted on the development...thanks a lot :)
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