[gmx-users] Meaning of n-n hydrogen bond

[ksr at chemistry.umass.edu]

Chetana,

You need to look at the structure of these residues. Several amino acids,
notably Asp and Asn can i to i sidechain to backbone h-bond. For those two it
typically occurs in the alphaL conformational space (what David was alluding
to), which is why Asp and Asn are (relatively) often found there.

Peace,

Ken

On Apr 25, 2007
Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> chetana baliga wrote:
> > Dear gmx users,
> >
> > Upon using g-hbond with the -hx option, to calculate hydrogen bonds in
> > the mainchain, we are supposed to get a list of all n-n+1 hydrogen
> > bonds, with i = 0 - 6. But, I am regularly getting several n-n
> > hydrogen bonds. What is the meaning of a hydrogen bond of a residue
> > with itself ! I am unable to understand, please help :)
> >
> > Thanks in advance,
> >
> > Chetana.
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> it can happen depending on backbone conformation.
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>