[gmx-users] g_mindist

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear Justin,
> 
> You said before "you can obtain some idea by using g_mindist to 
> calculate hydrophobic and hydrophilic contacts between the protein and 
> ligand".
> 
> That is, I can explore whether there is hydrophobic or hydrophilic 
> feature of ligand using g_mindist tool. is this correct?
> I did the calculations related to protein_ligand interactions (protein 
> contains two ligand). I plotted the graphs of distance and numcount 
> versus simulation time for each ligand. The number of contacts in  
> ligand x is more than the other ligand y. Which of this ligands are 
> hydrophobic? Which is hydrophilic? I know you are not private tutor. 
> Please don't be angry :(
> 

I certainly hope I haven't given the impression that I'm some angry tyrant.  I'm 
happy to answer reasonable questions across the list, time permitting.

To obtain information about hydrophobic and hydrophilic contacts, you need to 
use special index groups that tell g_mindist (or any other tool) which atoms to 
consider.  In this way, you can count how many of each type of contact evolve 
over time.

-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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