[gmx-users] validation of ligand parameters

Yun Shi yunshi09 at gmail.com
Fri Aug 12 16:08:41 CEST 2011

Hi all,

I have thought of three experimental values to validate the parameters I
assigned for a oligosaccharide, namely, free enthalpy of solvation, nOe
effect, and some J3-couplings.

For free enthalpy of solvation, I wondered why delta G was used to indicate
enthalpy? Would what be measured is just the heat, i.e., delta H ?

For nOe effect, should I use g_rmsdist to calculate 1/r3 and 1/r6 averaged
distances? Should I correlate these values to corresponding nOe initial
build-up rate or just a normal "steady-state" NOE?

For J-couplings, I cannot find a tool within GROMACS to do this. The command
g_chi only computes NMR 3J coupling constants for amino acid backbond and
sidechain atoms?

Thanks for any suggestion!

Yun Shi
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