normal forward mapping for Charmm36 TIP3

  • ngandhi
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7 years 1 week ago #7174 by ngandhi
forward mapping for Charmm36 TIP3 was created by ngandhi
Dear list,

I am trying to use backward.py to convert charmm36 to martini. My system consists of two DPPC monolayers and water. While the mapping is available for DPPC (from charmm36 to martini), it seems there is no mapping for the TIP3 solvent. I created a file sol.charmm36.map (below) but I have no luck converting atomistic coordinates to CG. Your help is appreciated.

[ molecule ]
TIP3

[ martini ]
W

[ atoms ]

1 OW W

2 HW1 W

3 HW2 W

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7 years 1 week ago #7185 by riccardo
Replied by riccardo on topic forward mapping for Charmm36 TIP3
I don't see any particular problem with your mapping file. Can you provide more details (e.g., the command you used, which error you got, etc.). And, does forward-mapping only the DPPC layers work?

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7 years 1 week ago - 7 years 1 week ago #7186 by riccardo
Replied by riccardo on topic forward mapping for Charmm36 TIP3
EDIT: see Tsjerk's reply.
Last edit: 7 years 1 week ago by riccardo.

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7 years 1 week ago #7188 by tsjerk
Replied by tsjerk on topic forward mapping for Charmm36 TIP3
Each water molecule should map to a quarter of a W bead. There is no way to do that with this type of mapping. My suggestion would be to remove the solvent, do the forward mapping and then add solvent with insane.

Cheers,

Tsjerk

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