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System setup with amphipol A8-35 polymer
- almeida
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7 years 8 months ago #5751
by almeida
System setup with amphipol A8-35 polymer was created by almeida
Hi all,
I want to run a simulation of a membrane protein with amphipol A8-35 polymer, similar to the work 10.1007/s00232-014-9690-8.
I have a new .itp file for A8-35 and I want to add different amounts of the A8-35 molecules randomly positioned in the simulation box, as part of the solvent.
Any idea about how to do it?
Thanks in advance
Yasser
I want to run a simulation of a membrane protein with amphipol A8-35 polymer, similar to the work 10.1007/s00232-014-9690-8.
I have a new .itp file for A8-35 and I want to add different amounts of the A8-35 molecules randomly positioned in the simulation box, as part of the solvent.
Any idea about how to do it?
Thanks in advance
Yasser
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- mnmelo
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7 years 8 months ago #5752
by mnmelo
Replied by mnmelo on topic System setup with amphipol A8-35 polymer
Hi Yasser,
I suggest you follow the same procedure as we describe in the bilayer self-assembling tutorial , but instead of randomly placing lipids, you randomly place your polymer.
Good luck and let us know how it goes,
Manel
I suggest you follow the same procedure as we describe in the bilayer self-assembling tutorial , but instead of randomly placing lipids, you randomly place your polymer.
Good luck and let us know how it goes,
Manel
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- almeida
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7 years 8 months ago #5755
by almeida
Replied by almeida on topic System setup with amphipol A8-35 polymer
Thanks!
In my case I don't have a .gro file for A8-35. I tried to run molmaker.py to convert the .itp to .gro but the script doesn't contains the martini ff.
Any idea how to convert .itp to CG .gro?
In my case I don't have a .gro file for A8-35. I tried to run molmaker.py to convert the .itp to .gro but the script doesn't contains the martini ff.
Any idea how to convert .itp to CG .gro?
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7 years 8 months ago #5756
by mnmelo
Replied by mnmelo on topic System setup with amphipol A8-35 polymer
Indeed molmaker.py is the way to go. If you download the
martini definition file
and place it in the same directory, then pass the optionto molmaker.
Note that I'm linking to the Martini 2.2 version. This should be what you need, but do check if other versions suit your purpose better.
-ff martini_v2.2.itpNote that I'm linking to the Martini 2.2 version. This should be what you need, but do check if other versions suit your purpose better.
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7 years 8 months ago #5757
by almeida
Replied by almeida on topic System setup with amphipol A8-35 polymer
It works!
Thanks
Thanks
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