1. Force Fields
  3. Other Molecules
  5. Hydration free energy of Lidocaine

normal Hydration free energy of Lidocaine

  • yogi@martini
  • yogi@martini's Avatar Topic Author
  • Offline
  • Junior Boarder
More
1 year 4 months ago #9549 by yogi@martini
Hydration free energy of Lidocaine was created by yogi@martini
Hello,

I am getting hydration free energy for Lidocaine as -104 kJ/mol. However it is a lipophilic molecule, with logP (octanol-water) = 2.26, and logS = -1.76 (solubility), the solubility value tells that it is soluble in water. However I am wondering whether such a high value of hydration free energy is correct.

the itp of Lidocaine generated by auto-martini, that I am using.
;;;; GENERATED WITH auto-martini and iteratively optimised against AA simulation
; INPUT SMILES: CCN(CC)CC(=O)NC1=C(C)C=CC=C1C
; Tristan Bereau (2014)

[moleculetype]
; molname nrexcl
LID 2

[atoms]
; id type resnr residu atom cgnr charge smiles
1 C5 1 LID C01 1 0 ; CC
2 C5 1 LID C02 2 0 ; CC
3 P2 1 LID P01 3 0 ; CN
4 P3 1 LID P02 4 0 ; NC=O
5 SC4 1 LID S01 5 0 ; Cc1ccccc1
6 SC5 1 LID S02 6 0 ; c1ccccc1
7 SC4 1 LID S03 7 0 ; Cc1ccccc1

[bonds]
; i j funct length force.c.
1 3 1 0.24 1250
2 3 1 0.24 1250
3 4 1 0.26 1250
4 7 1 0.25 1250

[constraints]
; i j funct length
5 6 1 0.24
5 7 1 0.24
6 7 1 0.24

[angles]
; i j k funct angle force.c.
1 3 2 2 60.2 27.0
1 3 4 2 104.5 32.0
2 3 4 2 120.0 29.0
3 4 7 2 98.6 61.0
4 7 5 2 60.4 22.0
4 7 6 2 120.1 25.0

Kindly give inputs on whether this value is reasonable, the -ve value as well as magnitude.

Thanks

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

More
1 year 4 months ago #9552 by riccardo
Replied by riccardo on topic Hydration free energy of Lidocaine
Did you compute the logP? Martini is not parametrized to reproduce hydration (or, in general, solvation) free energies but rather transfer free energies (aka partitioning free energies).

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

  1. Force Fields
  3. Other Molecules
  5. Hydration free energy of Lidocaine
Time to create page: 0.137 seconds