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forward mapping for Charmm36 TIP3
- ngandhi
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7 years 1 month ago #7175
by ngandhi
forward mapping for Charmm36 TIP3 was created by ngandhi
I have a system with two monolayers of DPPC and TIP3P water obtained from CHARMM_GUI. CHARMM-GUI doesn't support conversion of monolayers to Martini CG. I am trying to do forward mapping using the backward.py and it seems there is not Mapping file for TIP3P solvent. I renamed TIP3 to SOL. I tried to prepare the sol.charmm36.map file however it didn't work.
The command used was
backward.py -f test.pdb -o tt.gro -to martini -from charmm36 -po test.top -sol
Here is the mapping file
[ molecule ]
SOL
[ martini ]
W
[ atoms ]
1 OW W
2 HW1 W
3 HW2 W
The command used was
backward.py -f test.pdb -o tt.gro -to martini -from charmm36 -po test.top -sol
Here is the mapping file
[ molecule ]
SOL
[ martini ]
W
[ atoms ]
1 OW W
2 HW1 W
3 HW2 W
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- peterkroon
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7 years 4 weeks ago #7202
by peterkroon
Replied by peterkroon on topic forward mapping for Charmm36 TIP3
My suggestion is to remove all the waters, do the forward mapping of the lipids to Martini, and resolvate with Martini water using the normal gromacs tools.
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