normal reverse-mapping mthods

  • roshanak
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2 years 5 months ago - 2 years 5 months ago #6630 by roshanak
reverse-mapping mthods was created by roshanak
Hi.
i’m beginner in simulation. i’m doing membrane protein tutorial (kalp in dppc) that’s in this website.
I reach to reverse-mapping step. I think that i don’t understand correctly backmapping methods. i use this command:
$./backward.py -f CG.gro -o AA.gro -p systemCG.top -from martini -to charmm36

in AA.gro exists lipids and ions but it hasn’t protein and water. In this file, Lipids are coarse-grained yet.
What files do I need? I copy mapping folder, backward.py and initram.sh in my directory. I have files correspond to force field too.
Where is my wrong?
Last edit: 2 years 5 months ago by roshanak.

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2 years 4 months ago #6849 by riccardo
Replied by riccardo on topic reverse-mapping mthods
Hi roshanak,

I suggest you to do the backmapping tutorial first and then go back to the reverse-mapping step in the KALP one.

Btw, the backmapping command should look like this:
$ ./initram.sh -f CG_martini.gro -o aa_charmm.gro  -p system_AA.top -from martini -to charmm36

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2 years 4 days ago - 2 years 4 days ago #7282 by roshanak
Replied by roshanak on topic reverse-mapping mthods
Hi
again I need to reverse transform my system. I study tutorial. when I use initram.sh command, I receive this message:
initram.sh version 0.1:
(c)2013 Tsjerk A. Wassenaar, PhD
University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4
Now executing...
./initram.sh -f md300.pdb -o aa2-gromos.gro -from martini -to gromos54a7 -p topol.top
Checking dependencies:
backward.py ... Missing dependency: backward.py


when I try with backward.py command, has been made all atom scale of my system. but some atoms in top and aa.gro doesn't match. such as ASP has an addition atom . I use gromos54a7 to making top file and use gromos for mapping (in this command : ./backward.py -f md300.pdb -o aa-gromos.gro -from martini -to gromos54a7)
Would you please guide me?
Last edit: 2 years 4 days ago by roshanak.

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1 year 11 months ago - 1 year 11 months ago #7283 by riccardo
Replied by riccardo on topic reverse-mapping mthods

backward.py ... Missing dependency: backward.py


I guess this means that backward.py is not in the same folder as your initram.sh when you run initram.sh.

but some atoms in top and aa.gro doesn't match. such as ASP has an addition atom . I use gromos54a7 to making top file and use gromos for mapping


did you check whether this is consistent with the mapping files you find in the folder "Mapping" (you should have downloaded this folder along with backward.py and initram.sh), in particular the asp.gromos.map (I suppose)? The aa.gro generated is based on the mapping files.
Last edit: 1 year 11 months ago by riccardo.

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1 year 11 months ago - 1 year 11 months ago #7284 by roshanak
Replied by roshanak on topic reverse-mapping mthods
Thanks for reply

I guess this means that backward.py is not in the same folder as your initram.sh when you run initram.sh.


I had initram.sh and backward.py in a same folder.

did you check whether this is consistent with the mapping files you find in the folder "Mapping" (you should have downloaded this folder along with backward.py and initram.sh), in particular the asp.gromos.map (I suppose)? The aa.gro generated is based on the mapping files.



I downloaded a backward folder consistent backward.py and initram.sh and Mapping. In the mapping folder, in asp.gromos.map, I saw that asp has an addition atom ( 7 HD2 SC1), but in topol.top that made with gromos force field (with pdb2gmx and choosing gromos54a7) , asp is different.
Last edit: 1 year 11 months ago by roshanak.

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1 year 11 months ago - 1 year 11 months ago #7289 by riccardo
Replied by riccardo on topic reverse-mapping mthods
I'm not very familiar with the amino acids topology in GROMOS and do not know therefore which one is the right one -- since it's just an hydrogen, it could actually be a difference in protonation state. Anyway, have you tried checking the GROMOS 54A7 paper to find out? Based on that, you can edit the mapping file to get the mapping that you need to get.
Last edit: 1 year 11 months ago by riccardo.

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