[gmx-users] g_lie + running MDS for a ligand only

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 15 11:54:33 CEST 2008

vivek sharma wrote:
> Hi All,
> I want to use g_lie function of gromacs to calculate the binding free 
> energy og a ligand with the protein. For the same I need to run two MDS, 
> one for ligand only and one for ligand+protein complex (please correct 
> if I am wrong).
> What are the checks that I should take care in this case, e.g. Do I need 
> to keep the same box size, or same number of solvation molecule in two 
> cases ?
> or similar things.
> And also I am unable to run the MDS for ligand only as it gives the 
> error like.
> ...Residue 'D4N' not found in residue topology database.....

You're running pdb2gmx on the structure containing the protein and the ligand, 
aren't you?


> For the ligand+protein complex I followed the drug-enzyme tutorial by J 
> E Kerrigan, and it worked well.

Then you should be able to translate those same exact steps into how you should 
treat your situation, alleviating the above problem.

> How can I run the MDS for ligand only ?................................ 
> If I will take the .itp from the PRODRG and use it as .top and bypass 
> the pdb2gmx step as mentioned in the tutorial, will it work ? (consider 
> the difference in two cases one is ligand only and other is 
> ligand+protein ).

Yes.  In fact, PRODRG gives a .top, not an .itp file.  The modifications are 
explained in the tutorial you refer to.

Be aware that the charges and charge groups assigned by PRODRG often require 
modification before they are considered satisfactory.


> Please suggest...
> With Thanks,
> Vivek
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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