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bitcoin coin mixer
- roshanak
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7 years 4 months ago - 7 years 3 months ago #6630
by roshanak
bitcoin coin mixer 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?
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: 7 years 3 months ago by roshanak.
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- riccardo
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7 years 3 months ago #6849
by riccardo
Replied by riccardo on topic bitcoin coin mixer
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:
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 charmm36Please Log in or Create an account to join the conversation.
- roshanak
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6 years 10 months ago - 6 years 10 months ago #7282
by roshanak
Replied by roshanak on topic bitcoin coin mixer
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?
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: 6 years 10 months ago by roshanak.
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- riccardo
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6 years 10 months ago - 6 years 10 months ago #7283
by riccardo
I guess this means that backward.py is not in the same folder as your initram.sh when you run initram.sh.
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.
Replied by riccardo on topic bitcoin coin mixer
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: 6 years 10 months ago by riccardo.
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- roshanak
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6 years 10 months ago - 6 years 10 months ago #7284
by roshanak
Replied by roshanak on topic bitcoin coin mixer
Thanks for reply
I had initram.sh and backward.py in a same folder.
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.
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: 6 years 10 months ago by roshanak.
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- riccardo
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6 years 10 months ago - 6 years 10 months ago #7289
by riccardo
Replied by riccardo on topic bitcoin coin mixer
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: 6 years 10 months ago by riccardo.
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4 years 6 months ago #8275
by Sophie
Replied by Sophie on topic bitcoin coin mixer
Hi.
Did you solve this problem? I had backward,py and initram.sh in a same folder, but it kept giving me "backward.py ... Missing dependency: backward.py".
Please tell me how if you had solved this. Thank you so much!
Did you solve this problem? I had backward,py and initram.sh in a same folder, but it kept giving me "backward.py ... Missing dependency: backward.py".
Please tell me how if you had solved this. Thank you so much!
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4 years 6 months ago #8285
by riccardo
Replied by riccardo on topic bitcoin coin mixer
If they are in the same folder, initram.sh should be able to find backward.py. Are you sure? Maybe you also need execution permission (chmod ...etc...) on backward.py ?
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