From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue May 04 2004 - 13:20:20 CDT

Hi Ahmet,

That script is pretty involved. Now I understand what you want to do.
The most robust way I have done the hbond calculation is to make a list
of all donors and acceptors to start with.
But this is already known in VMD to a limited extent, ie all bonds are
stored at load up.

It is a matter of accessing that bond list in a
coherent way that makes the script a little tricky.

I would suggest looking at the way bond-lists are stored and accessed with
tcl commands like molinfo etc ....

Regards
Brian

On Tue, 4 May 2004, Ahmet Bakan wrote:

> Hi Brian and All,
>
> I thank you a lot and feel bed to cause a large email traffic for such a
> simple question :(
> I am sending the TCL script and showed where and why I want to make this
> selection. If you have any better ideas, I would like to hear.
>
> Thanks again,
>
> Ahmet
>
> ==========ABC==========
> Ahmet Bakan
> Chemistry, Junior
> Koc University
> abakan_at_ku.edu.tr
> ICQ #86167698
> http://home.ku.edu.tr/~abakan
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Brian Bennion
> Sent: Monday, May 03, 2004 10:14 PM
> Cc: 'VMD-L'
> Subject: RE: vmd-l: Selection problem on TkCon
>
>
> Can you just add another macro for oxygen, and sulfur?
>
> ie set connected [atomselect top "((same residue as ([$HATOM text])) and
> nitrogen) or ((same residue as ([$HATOM text])) and oxygen)"]
>
> Or have am I just completely confused?
>
> Brian
>
>
>
> On Mon, 3 May 2004, Ahmet Bakan wrote:
>
> > Hi Brian and All,
> >
> > set connected [atomselect top "(same residue as ([$HATOM text])) and
> > nitrogen"]
> > brings me the nitrogen atom that my H is bonded to and other N atoms if
> > there is.
> > What I exactly need is the atom H is bonded to, which may be any types O
> or
> > N.
> > I load PSF file and it has the list of each bond, is there a command makes
> > use of this?
> >
> > Thanks,
> >
> > Ahmet
> >
> > ==========ABC==========
> > Ahmet Bakan
> > Chemistry, Junior
> > Koc University
> > abakan_at_ku.edu.tr
> > ICQ #86167698
> > http://home.ku.edu.tr/~abakan
> >
> > -----Original Message-----
> > From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
> Of
> > Brian Bennion
> > Sent: Monday, May 03, 2004 6:14 PM
> > Cc: 'VMD-L'
> > Subject: RE: vmd-l: Selection problem on TkCon
> >
> > Hi Ahmet,
> >
> > Just add another qualifier in your selection statement or lsort the list
> > that "connected" gives you.
> >
> > ie..
> >
> > set connected [atomselect top "(same residue as ([$HATOM text])) and
> > nitrogen"]
> >
> >
> > Regards,
> > Brian
> >
> > On Mon, 3 May 2004, Ahmet Bakan wrote:
> >
> > > Hi Justin and All,
> > >
> > > I need the index of the single atom that hydrogen is bonded to.
> > > Like this
> > > -NH-CH2-CO-O-
> > > I have the index of H bonded to N, hundereds of H similar indices.
> > > I need index of N atom in this example.
> > >
> > > I tried this:
> > > set HATOM [atomselect top "index 547"]
> > > Result: H
> > > set connected [atomselect top "same residue as ([$HATOM text])"]
> > > Result: NH1 H CT1 HB CT2 HA HA CT2 HA HA CC O NH2 H H C O
> > > set connected [atomselect top "same bond as ([$HATOM text])"]
> > > Result: nothing happens
> > >
> > > Does anyone have idea?
> > > Thanks,
> > >
> > > Ahmet
> > >
> > >
> > > ==========ABC==========
> > > Ahmet Bakan
> > > Chemistry, Junior
> > > Koc University
> > > abakan_at_ku.edu.tr
> > > ICQ #86167698
> > > http://home.ku.edu.tr/~abakan
> > >
> > > -----Original Message-----
> > > From: Justin Gullingsrud [mailto:jgulling_at_mccammon.ucsd.edu]
> > > Sent: Monday, May 03, 2004 11:36 AM
> > > To: Ahmet Bakan
> > > Cc: VMD-L
> > > Subject: Re: vmd-l: Selection problem on TkCon
> > >
> > > Hi,
> > >
> > > On Mon, May 03, 2004 at 03:55:43AM +0300, Ahmet Bakan wrote:
> > > > Hi All,
> > > >
> > > >
> > > >
> > > > I have a selection of Hydrogen atoms and I want to get the list of
> atoms
> > > > that Hydrogens in my selection are attached to. How can this be done
> on
> > > > TkCon?
> > >
> > > I assume you have a selection that you created from the text console,
> > > something like this:
> > >
> > > set sel [atomselect top "hydrogen and resname ALA"]
> > >
> > > Whatever the selection is, you can find all the atoms in the same
> > > residue as the selection by typing the following:
> > >
> > > set connected [atomselect top "same residue as ([$sel text])"]
> > >
> > > You can then write out a list of atoms in the selection to a file with:
> > >
> > > set fd [open connatoms.ind w]
> > > foreach ind [$connected list] { puts $fd $ind }
> > > close $fd
> > >
> > > Note that the indicies written to the file will be one smaller than the
> > > corresponding atom in a pdb file; i.e., they will be 0-based rather than
> > > 1-based.
> > >
> > > Cheers,
> > > Justin
> > >
> > > >
> > > >
> > > >
> > > > Cheers,
> > > >
> > > > Ahmet
> > > >
> > > >
> > > >
> > > > ==========ABC==========
> > > >
> > > > Ahmet Bakan
> > > >
> > > > Chemistry, Junior
> > > >
> > > > Koc University
> > > >
> > > > abakan_at_ku.edu.tr
> > > >
> > > > ICQ #86167698
> > > >
> > > > http://home.ku.edu.tr/~abakan
> > > >
> > > >
> > > >
> > >
> > > --
> > >
> > > Tenth is 10 spots too low as far as I'm concerned. -- George W. Bush
> > >
> >
> > *****************************************************************
> > **Brian Bennion, Ph.D. **
> > **Computational and Systems Biology Division **
> > **Biology and Biotechnology Research Program **
> > **Lawrence Livermore National Laboratory **
> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> > **7000 East Avenue phone: (925) 422-5722 **
> > **Livermore, CA 94550 fax: (925) 424-6605 **
> > *****************************************************************
> >
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************