Converting all atom to coarse grained with backward.py
- Hot
-
Topic Author
- Visitor
4 years 6 months ago #8306
by Hot
Converting all atom to coarse grained with backward.py was created by Hot
The all-atom simulation uses the GAFF force field，which is converted from AMBER to gromacs format by ACPYPE.
I want to convert all atom to coarse grained with backward.py, while the GAFF force field was not found in backward.
After running do-mapping.sh, it looks like this: Residues defined for transformation from gromos to martini. How can I modify it before I can continue to use backward?
I want to convert all atom to coarse grained with backward.py, while the GAFF force field was not found in backward.
After running do-mapping.sh, it looks like this: Residues defined for transformation from gromos to martini. How can I modify it before I can continue to use backward?
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
Less
More
4 years 6 months ago - 4 years 6 months ago #8308
by riccardo
Replied by riccardo on topic Converting all atom to coarse grained with backward.py
I don't know the specifics of the script you are using (which I think is from a tutorial) but make sure that you call backward.py by saying "-from amber -to martini" and that Mapping files for the amber-martini conversion exists.
Pasting the actual commands used here in the forum would also help debugging.
Pasting the actual commands used here in the forum would also help debugging.
Last edit: 4 years 6 months ago by riccardo.
Please Log in or Create an account to join the conversation.
- Hot
-
Topic Author
- Visitor
4 years 6 months ago - 4 years 6 months ago #8309
by Hot
Replied by Hot on topic Converting all atom to coarse grained with backward.py
Yeah，it is from the tutorial. I've changed it to "-from amber -to martini", it appears:
Problem determining mapping coordinates for atom NA1 of residue DAT.
atomlist: （'TP1', 'NA1', 'TC1', 'TC2', 'TC3'）
want: NA1 （'C10', 'H8', 'H9', 'O4', 'C9', 'O3'）
have: （'H2', 'H3', 'O5', 'H6', 'C1'）
Bailing out...
（NA1', 'TC1', 'TC2', 'TC3'）
Problem determining mapping coordinates for atom NA1 of residue DAT.
atomlist: （'TP1', 'NA1', 'TC1', 'TC2', 'TC3'）
want: NA1 （'C10', 'H8', 'H9', 'O4', 'C9', 'O3'）
have: （'H2', 'H3', 'O5', 'H6', 'C1'）
Bailing out...
（NA1', 'TC1', 'TC2', 'TC3'）
Last edit: 4 years 6 months ago by Hot. Reason: don't show
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
4 years 5 months ago #8314
by riccardo
Replied by riccardo on topic Converting all atom to coarse grained with backward.py
This is always a little cryptic; you should look at the labels mentioned and whether they make sense. This means, have a look at the mapping file (in folder "Mapping") for the residue DAT and check whether those atom labels make sense (both the atomistic and the CG ones): there must be something wrong there.
Please Log in or Create an account to join the conversation.
Time to create page: 0.091 seconds