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Martinizing lipid molecules
- jmondal
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8 years 1 month ago #5404
by jmondal
Martinizing lipid molecules was created by jmondal
Dear Martini-users
I wanted to transform a snapshot of my atomistic DPPG/water bilayer to the CG format. However, I found martinize.py script does not transform lipid or waters to coarse-grained counterpart.It only works for protein. So, Is there any particular way I can generate the CG version of my atomistic DPPG/water bilayer ?
I guess backward scripts does the reverse of what I am trying to achieve. So, if you can suggest a way to generate a coarse-grained pdb files of the atomistic lipid bilayer/water, that will be very helpful.
Jagannath
I wanted to transform a snapshot of my atomistic DPPG/water bilayer to the CG format. However, I found martinize.py script does not transform lipid or waters to coarse-grained counterpart.It only works for protein. So, Is there any particular way I can generate the CG version of my atomistic DPPG/water bilayer ?
I guess backward scripts does the reverse of what I am trying to achieve. So, if you can suggest a way to generate a coarse-grained pdb files of the atomistic lipid bilayer/water, that will be very helpful.
Jagannath
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- mnmelo
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8 years 1 month ago #5410
by mnmelo
Replied by mnmelo on topic Martinizing lipid molecules
Hi Jaganath,
The backward.py script also does precisely what you want. Just set the -from flag to
"martini" and the -to flag to your atomistic force field (assuming you have all the needed mapping files).
The backward.py script also does precisely what you want. Just set the -from flag to
"martini" and the -to flag to your atomistic force field (assuming you have all the needed mapping files).
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- yogi@martini
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6 years 9 months ago - 6 years 9 months ago #7309
by yogi@martini
Replied by yogi@martini on topic Martinizing lipid molecules
Hello mnmelo,
Thanks for the answer. Can you please elaborate more about atomic to cg conversion using backword.py
1. Where does we define mapping. How to create that file manually. I remember older version of gromacs had [mapping] column in topology file. Can we do similar thing in backword.py
2. If we want to assign desired bead manually and don't need it to be done automatically. How to do it.
3. Can you please give example command about running backward.py
from your above answer, is it like
python backward.py -f atomistic.gro -o cg.gro -from martini -to ?
how to set force field as you mentioned?
Any help will be much appreciated.
Thanks
Thanks for the answer. Can you please elaborate more about atomic to cg conversion using backword.py
1. Where does we define mapping. How to create that file manually. I remember older version of gromacs had [mapping] column in topology file. Can we do similar thing in backword.py
2. If we want to assign desired bead manually and don't need it to be done automatically. How to do it.
3. Can you please give example command about running backward.py
from your above answer, is it like
python backward.py -f atomistic.gro -o cg.gro -from martini -to ?
how to set force field as you mentioned?
Any help will be much appreciated.
Thanks
Last edit: 6 years 9 months ago by yogi@martini.
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- riccardo
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6 years 9 months ago #7310
by riccardo
Replied by riccardo on topic Martinizing lipid molecules
Hi Jagannath,
please make sure to follow this tutorial first:
www.cgmartini.nl/index.php/tutorials-gen...tion/others#Backward
It mostly covers all the questions you raised (the mapping files, the commands, etc.). However, you will then have to apply it in reverse (so switching the two flags, as suggested by Manel; again, you can find an example of complete command in the tutorial). Let us know if you still have more questions after the tutorial.
please make sure to follow this tutorial first:
www.cgmartini.nl/index.php/tutorials-gen...tion/others#Backward
It mostly covers all the questions you raised (the mapping files, the commands, etc.). However, you will then have to apply it in reverse (so switching the two flags, as suggested by Manel; again, you can find an example of complete command in the tutorial). Let us know if you still have more questions after the tutorial.
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