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

[Dina Mirijanian]

Oh, I see.  So the -contact flag calculates all contacts within the cutoff
distance and does not care if an atom is a donor or acceptor.
-Dina

On Thu, Oct 29, 2015 at 4:07 PM, Dina Mirijanian <dmirij at brandeis.edu>
wrote:

> 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
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>