[gmx-users] help

shikhar gupta shik_sun at rediffmail.com
Mon Apr 19 11:39:34 CEST 2010

Hi gmx users,

I used g_lie command to compute free energy.
The command and the output is as follow

[shikhar at venus 30078-dyn10ns]$ g_lie -f edr.edr -ligand UNK -o lie10ns.xvg

-ligand string UNK Name of the ligand in the energy file

Opened edr.edr as single precision energy file
Using the following energy terms:
LJ: LJ-SR:Protein-UNK LJ-LR:Protein-UNK LJ-14:Protein-UNK LJ-SR:SOL-UNK LJ-LR:SOL-UNK LJ-14:SOL-UNK LJ-SR:UNK-rest LJ-LR:UNK-rest LJ-14:UNK-rest
Coul: Coul-SR:Protein-UNK Coul-14:Protein-UNK Coul-SR:SOL-UNK Coul-14:SOL-UNK Coul-SR:UNK-rest Coul-14:UNK-rest
Last frame read 50000 time 10000.000
DGbind = -88.393 (5.098)

gcq#306: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)

The value is coming DGbind = -88.393 (5.098).
Whether this is correct method to get the free energy of binding of a ligand.
Any other command or method is there to get the free energy of binding of ligands or can we do the MM/PBSA and MM/GBSA analysis from the gromacs dynamics.

Shikhar Gupta
Senior Research Fellow
Pharmacoinformatics Department
Block- A (Room No.- 208)
National Institute of Pharmaceutical Education & Research( NIPER )
Sec- 67, S.A.S Nagar
Mohali, Punjab (India)
Web-Site: www.niper.ac.in
PIN- 160062
Email:shik_sun at rediffmail.com,shiksun at gmail.com
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