[gmx-users] Re: Interaction energy between specific residue in a set of residues

[Collins Nganou]

Hi Tomas,

I am sorry to come with this further problem of gromacs.

I would like to plot an interaction energy between DT without include DA.
But I do not know how to ask make g_energy read my index file. Furthermore,
I was interested of the distance between C5-C6 in adjacent DT. But I do not
know how to ask make_ndx to read C5-C6 in DT with looking for the DA.

Please If you can suggest me something it will be great for me.

I wish you a wonderful day.


Collins




On Wed, Jul 31, 2013 at 4:20 PM, Collins Nganou <nganoucollins at gmail.com>wrote:

>
> Dear all,
>
> I am looking how  I can extract the interaction energy between  specific
> residue in a set of  residues.
>
> example:
>
> I have DT and DA residues, I would like to plot only the energy of the DT.
> I can extract the DT with the index file, But I am missing information on
> how to plot the energy base on my index file where I can select only DT.
>
> I was only looking the way to extract the c5-c6 distance of adjacent DT
> without include DA.
>
> I will be very grateful to receive any suggestions....
>
>
>
> I wish you all a wonderful day...
>
> Collins
>
>