VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Tue Jun 05 2007 - 20:57:11 CDT

Hi Axel, yes, I was referring to 'molecule' in the VMD sense, I'm aware
of this. I was wondering if there was a way to do this, without merging
the files (because I have a lot of structures, and this might become
cumbersome).

But, if that's the way I have to do it, then so be it . . . thanks,

Arneh

Axel Kohlmeyer wrote:
> On Tue, 5 Jun 2007, Arneh Babakhani wrote:
>
> AB> Hi,
> AB>
> AB> Is there a way to measure hbonds between selections that are from
> AB> different molecules? I ask, b/c I noticed that in the manual, it states
> AB> that to use 'measure hbonds', selections must be from the same molecule.
>
> it is in the manual, because this is how it is implemented.
>
> however, molecule is to be understood in the VMD sense of a molecule,
> i.e. the coordinates have to be read from the same file. which is
> not the same molecule in the chemical sense.
>
> if you have two different VMD molecules (i.e. want to compare hydrogen
> bonds between two different files), you'll have to merge the files and
> read the resulting file into VMD.
>
> hope that clarifies it.
>
> cheers,
> axel.
>
>
> AB>
> AB> Thanks,
> AB>
>
>