[From nobody Thu Nov 14 11:52:41 2013
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Subject: =?utf-8?B?aGVscA==?=
From: "shikhar gupta"<shik_sun@rediffmail.com>
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Hi gmx users,

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

[shikhar@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@rediffmail.com,shiksun@gmail.com
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Hi gmx users,<br />
<br />
I used g_lie command to compute free energy.<br />
The command and the output is as follow<br />
<br />
[shikhar@venus 30078-dyn10ns]$ g_lie -f edr.edr -ligand UNK -o lie10ns.xvg<=
br />
<br />
-ligand string UNK Name of the ligand in the energy file<br />
<br />
Opened edr.edr as single precision energy file<br />
Using the following energy terms:<br />
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<br />
Coul: Coul-SR:Protein-UNK Coul-14:Protein-UNK Coul-SR:SOL-UNK Coul-14:SOL-U=
NK Coul-SR:UNK-rest Coul-14:UNK-rest<br />
Last frame read 50000 time 10000.000<br />
DGbind =3D -88.393 (5.098)<br />
<br />
gcq#306: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)<br />
<br />
The value is coming DGbind =3D -88.393 (5.098).<br />
Whether this is correct method to get the free energy of binding of a ligan=
d.<br />
Any other command or method is there to get the free energy of binding of l=
igands or can we do the MM/PBSA and MM/GBSA analysis from the gromacs dynam=
ics.<br />
<br><br>------------------<br />
Shikhar Gupta<br />
Senior Research Fellow<br />
Pharmacoinformatics Department<br />
Block- A (Room No.- 208)<br />
National Institute of Pharmaceutical Education & Research( NIPER )<br />
Sec- 67, S.A.S Nagar<br />
Mohali, Punjab (India)<br />
Web-Site: www.niper.ac.in<br />
PIN- 160062<br />
Email:shik_sun@rediffmail.com,shiksun@gmail.com<br><Table border=3D0 Width=
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dle?" target=3D"_blank"><IMG SRC=3D"http://sigads.rediff.com/RealMedia/ads/=
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</Table>
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