[gmx-users] Re: Protein ligand simulation

[Justin A. Lemkul]

bharat gupta wrote:
> I checked the docked structure and the structure obtained after adding 
> the ligand coordinates to the processed file obtained after using 
> pdb2gmx command. It's very surprising that in the docked structure 
> ligand is at the correct place but the processed gromacs file the ligand 
> lies far apart from the protein. Any clue what could be the reason for 
> this ??
> 

If the docked structure is correct, and the one you reassembled is incorrect, 
you made some mistake in putting it back together.  It's impossible to say what 
went wrong based on the (lack of) information given.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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