Hi Dan,
The GitHub version works perfectly, thank you for the help and the quick
response!
On Wed, Oct 25, 2017 at 10:39 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You'll have to use the GitHub version of cpptraj
> (https://github.com/Amber-MD/cpptraj), which has the new
> 'bridgebyatom' keyword for 'hbond'; I think this will give you the
> output you want.
>
> Hope this helps,
>
> -Dan
>
> On Wed, Oct 25, 2017 at 11:22 AM, Amy Rice <arice3.hawk.iit.edu> wrote:
> > Hi all,
> > I have a membrane system with a large number of ions and am interested in
> > seeing which functional groups these ions are bridging. The use of
> > solventdonor, solventacceptor, and bridgeout keywords gives information
> on
> > which residues the ions are coordinating, but since I have very large
> > residue definitions this output does not provide the level of detail
> that I
> > am interested in. Is there any way to have hbond output which specific
> > atoms are involved in the interactions, rather than just which residues?
> > For example, the bridge output looks like this:
> > Bridge Res 227:HEP5 233:HEP5, 62502 frames.
> > Is there any way to make it something like this instead:
> > Bridge Res 227:HEP5.atoms_involved 233:HEP5.atoms_involved, 62502
> frames.
> >
> > Thank you for your help,
> > - Amy
> >
> > --
> > Amy Rice
> > Ph.D. Student
> > Physics Department
> > Illinois Institute of Technology
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Wed Oct 25 2017 - 09:00:04 PDT
