[gmx-users] Re: protein-ligand interactions in charmm force field

[James Starlight]

Justin,

Thanks again for suggestion. I've found that g_mindist is exactly what
I need. I'm not quite sure how I could use that tools to find all
possible interactions between my ligand and several polar residues
defined in the ndx file ( I have no problem only when I examined
manually each possible interaction separately). Finally I'm not quite
sure about number of contacts calculated by g_mindist. E.g I've
examined it for my ligand ( having 3 polar atoms and large hydrophobic
ring)  and 1 serine residue ( 1 polar side chain group ). As the
ouitput I've obtain 60 maximum contact number (and 10- minimum). Why
maximum number was so big ?

Some another question- I want to find a way to esstimate average
mobility of my ligands in the ligand binding pocket.
For example I have 2 different complexes of my protein with 2
different ligands- one of that liugand is big and occupy big spacy
whithin protein interiour ( so that ligand is less mobile). On the
contrary the second ligand is samller and flexible so it muast be more
mobile within protein and it seen visually during visualisation of the
md trajectory. But how it could be estimated in some values ?


Thanks for help

James

2013/2/7 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 2/6/13 2:54 PM, James Starlight wrote:
>>
>> by the way could someone provide me with some simple tutorial of the
>> usage of the CGenFF for construction ITP topology for charmm f.f ?
>>
>>
>> Also I still could not found any simple way to monitor dynamics of the
>> non-covalent interactions between ligand and ligand binding pocket.
>> E.g I select manually in the ndx file all residues which could be
>> involved in such interactions (including formation of  possible
>> h.bonds, salt bridges as well as stacking interactions ) in one group
>> and ligand inthe second group. Should I use combination of g_hbond and
>> g_saltbr tools for such identification? How stacking interactions
>> could be monitored?
>>
>
> g_hbond, g_dist, and g_mindist -on with clever use of index groups can
> address all of these.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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