Hi,
Unfortunately no, the only information that is tracked by hbond
bridging is the residue number. When I originally wrote the code this
was done to reduce the memory needed (since you're tracking residue
pairs instead of atom pairs, of which there can be many more of
course). It may be useful to add this in the future.
However, you can have atom numbers printed for the other average
output since this is tracked by specifying 'printatomnum'. This could
at least give you an idea of which atoms may be involved in bridging,
-Dan
On Wed, Sep 17, 2014 at 9:36 AM, Miroslav Krepl <krepl.seznam.cz> wrote:
> Dear Amber,
>
> I was wondering whether there is any way to make the cpptraj (my version
> is 14.09) print out atom names in its solvent bridge function.
>
> I use the following command:
>
> ---
>
> hbond WATERS out waters.out :$A,$B solventdonor :WAT
> solventacceptor :WAT avgout all.out
>
> ---
>
> The cpptraj prints everything correctly, however, the default format of
> the "#Bridging Solute Residues" data series is like:
>
> ---
>
> Bridge Res 50:C 78:A , 6573 frames.
>
> ---
>
> Is there any option to make the cpptraj print also the atom name in
> addition to the residue number and name? For example, to make it look
> like this:
>
> ---
>
> Bridge Res 50:C.OP1 78:A.OP1 , 6573 frames.
>
> ---
>
> Thank you very much for any advice.
>
>
> --Miroslav Krepl
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Sep 17 2014 - 10:00:02 PDT
