VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jun 27 2015 - 01:46:05 CDT

Notice, if relevant, that the system contained TIP3 water in a periodic box.

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sat, Jun 27, 2015 at 8:32 AM
Subject: Re: vmd-l: Removing all non polar hydrogens
To: Josh Vermaas <vermaas2_at_illinois.edu>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>

I tried your suggestion on the tk console after loading psf/pdb

loading history file ... 22 events added
Main console display active (Tcl8.5.6 / Tk8.5.6)
(tmp) 23 % set sel [atomselect top "noh or withinbonds 1 of name
\"[O,N].*\""]
invalid command name "O,N"
>Main< (tmp) 24 %

On Fri, Jun 26, 2015 at 9:55 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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
>
>
>