VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Jun 26 2015 - 14:55:56 CDT

How about "noh or withinbonds 1 of name \"[O,N].*\""? First part gets
you all the heavy atoms, second part saves hydrogens that are bonded to
oxygens or nitrogens. It will require you to load your psf or equivalent
topology-bearing file so the bond definitions are correct, but that
ought to be trivial anywhere (mol new blah.psf; mol addfile blah.pdb;)

-Josh Vermaas

On 6/26/15 12:57 PM, Francesco Pietra wrote:
> hello:
>
> is there an alternative to
>
> set sel [atomselect top "not hydrogen"]
> $sel writepdb ...
>
>
> in order to remove all non polar hydrogens only? Possibly without
> loading the psf file, that would be difficult in the context where i
> am now working.
>
> For example, with CHIMERA the command "delete HC" exists.
>
> thanks
>
> francesco pietra