- Posts: 3
Backward mapping for protein
- abhinavsri89
-
Topic Author
- Offline
- Fresh Boarder
Less
More
2 years 2 months ago #9308
by abhinavsri89
Backward mapping for protein was created by abhinavsri89
Hi Martini Users,
I have a CG system of protein in presence of POPC lipids. I am trying to backmap my CG system from martini to CHARMM36. Following is the command which I am using:
./initram-v5-1.sh -f system-12ms.gro -o AA-CHARMM.gro -to CHARMM36 -p topol.top
Following is the error which I am getting.
Checking dependencies:
backward.py ... /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/backward.py
gmx ... /usr/local/bin/gmx
/home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/backward.py -f system-12ms.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to CHARMM36
Error reading amber to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber94 to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber96 to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber99 to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber99sb to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber03 to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amberGS to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Residues defined for transformation from martini to charmm36:
Problem determining mapping coordinates for atom HG1 of residue GLY.
atomlist:
want: HG1
have:
Bailing out...
I have the mapping files which I have download from the tutorial.
Kindly find the dropbox link for the files
www.dropbox.com/sh/kgpzg3pc1200agm/AADz7...wLCHIeG-LXdrGHa?dl=0
Any help would be very much appreciated !
Thanks in advance !
Abhinav
I have a CG system of protein in presence of POPC lipids. I am trying to backmap my CG system from martini to CHARMM36. Following is the command which I am using:
./initram-v5-1.sh -f system-12ms.gro -o AA-CHARMM.gro -to CHARMM36 -p topol.top
Following is the error which I am getting.
Checking dependencies:
backward.py ... /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/backward.py
gmx ... /usr/local/bin/gmx
/home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/backward.py -f system-12ms.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to CHARMM36
Error reading amber to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber94 to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber96 to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber99 to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber99sb to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amber03 to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Error reading amberGS to martini mapping for GMO (file: /home/tuo83323/Desktop/Abhinav-work/sars-project/backmapping/Mapping/phe.charmm36.map).
Residues defined for transformation from martini to charmm36:
Problem determining mapping coordinates for atom HG1 of residue GLY.
atomlist:
want: HG1
have:
Bailing out...
I have the mapping files which I have download from the tutorial.
Kindly find the dropbox link for the files
www.dropbox.com/sh/kgpzg3pc1200agm/AADz7...wLCHIeG-LXdrGHa?dl=0
Any help would be very much appreciated !
Thanks in advance !
Abhinav
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
2 years 1 month ago #9327
by xavier
Replied by xavier on topic Backward mapping for protein
Hi,
It seems that there is an issue in the mapping. As you seem to give the CHARMM files it seems to be looking for the AMBER mapping.
any reason you can think of?
It seems that there is an issue in the mapping. As you seem to give the CHARMM files it seems to be looking for the AMBER mapping.
any reason you can think of?
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
2 years 1 month ago #9328
by xavier
Replied by xavier on topic Backward mapping for protein
Hi,
It seems that there is an issue in the mapping. As you seem to give the CHARMM files it seems to be looking for the AMBER mapping.
any reason you can think of?
It seems that there is an issue in the mapping. As you seem to give the CHARMM files it seems to be looking for the AMBER mapping.
any reason you can think of?
Please Log in or Create an account to join the conversation.
- abhinavsri89
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 3
2 years 1 month ago #9335
by abhinavsri89
Replied by abhinavsri89 on topic Backward mapping for protein
I am not very sure of the reason.
In the input command, I am specifying CHARMM forcefield to backmap. The mapping folder also has the mapping files for GLY.
I am kind of stuck in this problem.
Any help would be really appreciated.
In the input command, I am specifying CHARMM forcefield to backmap. The mapping folder also has the mapping files for GLY.
I am kind of stuck in this problem.
Any help would be really appreciated.
Please Log in or Create an account to join the conversation.
- midhun
-
- Offline
- Fresh Boarder
Less
More
- Posts: 2
2 years 2 weeks ago #9371
by midhun
Replied by midhun on topic Backward mapping for protein
Hello i have aproblem on backmapping cg martini. Im getting the following error
Residues defined for transformation from martini to charmm36:
dict_keys()
None
Problem determining mapping coordinates for atom HZ1 of residue SER.
atomlist:
want:
HZ1
should be mapping from:
have:
dict_keys()
Bailing out...
Residues defined for transformation from martini to charmm36:
dict_keys()
None
Problem determining mapping coordinates for atom HZ1 of residue SER.
atomlist:
want:
HZ1
should be mapping from:
have:
dict_keys()
Bailing out...
Please Log in or Create an account to join the conversation.
- midhun
-
- Offline
- Fresh Boarder
Less
More
- Posts: 2
2 years 2 weeks ago #9372
by midhun
Replied by midhun on topic Backward mapping for protein
Im also facing the same problem. Dont know how to rectify
Please Log in or Create an account to join the conversation.
- Balaban
-
- Offline
- Fresh Boarder
Less
More
- Posts: 1
1 year 11 months ago #9388
by Balaban
Replied by Balaban on topic Backward mapping for protein
I'm having same issue, I cant convert martini3 Gō-like protein to AA with backwards tool. This is really necessary when I want to have extra coverage with CHARMM36 FF after ligand-protein docking+complexation with martini3.
All-atom takes so much time and computational power when u want to run 1-2µs simulations or multiple simulations on single desktop computer. However martini3 is not really 100% reliable for me, I want to run extra 50ns all-atom simulations.
I hope this problem will be solved soon. Thank you :)
All-atom takes so much time and computational power when u want to run 1-2µs simulations or multiple simulations on single desktop computer. However martini3 is not really 100% reliable for me, I want to run extra 50ns all-atom simulations.
I hope this problem will be solved soon. Thank you :)
Please Log in or Create an account to join the conversation.
Time to create page: 0.095 seconds