[gmx-users] frequency of contact between all residue pairs

[Dina Mirijanian]

Hi Erik,

Thank you for the suggestion.  But, will this not only give me H-bond
contacts only? I am looking for any contact. The only way I can see to make
this work is to make all atoms donors and acceptors, and I do not know how
to do this.  Am I missing something or is there a simple way to do this?
Thanks so much.
-Dina

On Wed, Oct 21, 2015 at 11:09 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk
> wrote:

> Hi Dina,
>
> g_hbond -contact -hbn -hbm, then post-process the resulting contact matrix
> to represent residue-residue interactions.
>
> Kind regards,
> Erik
>
> Erik Marklund, PhD
> Postdoctoral Research Fellow
> Fulford JRF, Somerville College
>
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
>
> > On 21 Oct 2015, at 15:56, Dina Mirijanian <dmirij at brandeis.edu> wrote:
> >
> > Hello,
> >
> > I need to calculate the contact frequence between all pairs of residues
> in
> > my protein within a certain cutoff. I was trying to figure out a way to
> do
> > this with g_mindist.  But I have not been able to get it do what I want.
> > Can someone tell me what is the best way to calculate the contact
> frequence
> > between all residues from a trajectory?
> > Thank you so much.
> > -Dina
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