normal topology for Benzo[a]pyrene

  • Mike
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13 years 3 months ago #457 by Mike
topology for Benzo[a]pyrene was created by Mike
Hello All
I’m new to the MARTINI forcefield and at present I’m trying to prepare the topology for the benzo[a]pyrene molecule. Is it correct to apply the exact constraints and atom types describing benzene molecule to create the benzo[a]pyrene molecule or should I use other parameters/atom types?
Please give me some suggestions, thank you in advance.
I wish everybody a wonderful and happy New Year.
Mike

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13 years 3 months ago #458 by siewert
Replied by siewert on topic topology for Benzo[a]pyrene
It seems reasonable to take the same particle types and bonded parameters as for benzene. However, you have to add additional (dihedral) potentials to keep the overall geometry of this molecule planar. See for inspiration the cholesterol topology.

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