[gmx-users] g_mindist

ahmet yıldırım ahmedo047 at gmail.com
Sun Jul 3 00:00:23 CEST 2011

Dear Justin,

can you suggest me published paper related to about hydrophobic and
hydrophilic contacts?

03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

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