[gmx-users] Center of Mass (COM) spacing between protein and ligand

[Justin Lemkul]

On 5/13/13 5:33 AM, Arunima Shilpi wrote:
> Respected Sir
> many many thanks for your reply to my last mail. I was able able to debug
> the error
>
> Here I have new set of queries..
>
> How much COM spacing should i consider for my protein-ligand interactiom
> How much total distance I should move along z-axis/...
> and which all conf file should i take into consideration for
> npt_umbrella.mdp...
>
> I have   my summary_distance.dat as an attachment
>

Attachments are not allowed by the list, nor is this one particularly useful in 
any sense to anyone who's not familiar with your exact system.

> Here in your example I could not understand as to why have you taken conf0
> extending to con450 for ur npt_umbrella.mdp..
>
> I request you to kindly guide me to the next step...
>

I think you should spend some time familiarizing yourself with published 
literature on this topic.  There is a ton of information out there, and it 
really isn't possible to give someone step-by-step instructions via mailing 
list.  The mailing list archive does have some pieces of information that may be 
useful, but the literature should cover everything you need to know.

-Justin

-- 
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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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