normal Parameterizing new molecule

  • SNEHA
  • SNEHA's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
1 year 7 months ago #7220 by SNEHA
SNEHA created the topic: Parameterizing new molecule
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.

Please Log in or Create an account to join the conversation.

More
1 year 7 months ago #7227 by riccardo
riccardo replied the 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.

Please Log in or Create an account to join the conversation.

More
1 week 4 days ago #7916 by molashahi
molashahi replied the topic: Parameterizing new molecule
Dear Experts
How can I build a gro file for PEO(100 monomers?
Thanks

Please Log in or Create an account to join the conversation.

More
1 week 3 days ago #7918 by Pim
Pim replied the 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.

Please Log in or Create an account to join the conversation.

Time to create page: 0.100 seconds