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normal Parameterizing new molecule

  • SNEHA
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7 years 3 weeks ago #7220 by SNEHA
Parameterizing new molecule was created by SNEHA
I have been trying to parameterize a drug molecule. I wanted to know which bead types must be assigned for the following
1. trifluoromethyl (-CF3)
2. Piperidine ring with -CH2-CH3 at 2nd position
I have divided the ring as -
CCC1CCccN1
C1CccNC1
C1CccNC1
Kindly help me in this regard.

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7 years 2 weeks ago #7227 by riccardo
Replied by riccardo on topic Parameterizing new molecule
-CF3 is not a very standard fragment. Have you searched for partitioning data for, say, CHF3 or similar fragments? That would help you in choosing the right bead type.

I could not really understand how you divided the ring. However, I would you use 3 S-beads, probably 2 SC2s/SC3s and 1 SNa (involving the nitrogen). Again, experimental free energies of transfer would help to settle for a mapping which is consistent with experimental partitioning data.

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5 years 5 months ago #7918 by Pim
Replied by Pim on topic Parameterizing new molecule
There are so many ways... Considering EO is just 1 bead you can simply make a line of beads with every z coordinate increasing by the bond length. With gromacs tools you could use genconf to multiply a single bead gro file 100 times with displacement in 1 direction.

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  1. Force Fields
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  5. Parameterizing new molecule
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