VMD-L Mailing List

From: B. Bennion (bbennion_at_u.washington.edu)
Date: Fri Oct 11 2002 - 00:40:52 CDT

Hi Eric,

VMD at present does not have its own ability to read in coordinate files
in any xyz format. VMD relies on BABEL which is a program that translates
a host of file formats to something VMD can understand. The download
notes mention the fact that BABEL is needed.
Check out
http://smog.com/chem/babel/

to see if molden xyz files can be read by babel.

>From the format you show below, VMD is not going to be able to read it
without some kind of file that explains what residues the atoms belong to.

Email me directly if you have further questions.

regards,
Brian

 On Thu, 10 Oct 2002, eric hu wrote:

> Date: Thu, 10 Oct 2002 18:27:11 -0700 (PDT)
> From: eric hu <erichu_linux_at_yahoo.com>
> To: B. Bennion <bbennion_at_u.washington.edu>
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: molden xyz movie
>
> I don't know what you mean. I generated a movie file
> specifically for molden from a dynamics simulation and
> now I want to make a single movie file out of vmd
> which I can use for presentation. I don't know what
> kind of xyz format VMD requires. The molden xyz format
> is shown below:
> 90
>
> H 1.40991089 -2.21608925
> -1.67898951
> H 2.67237271 1.83803937
> -0.82090295
> H -3.03770597 -1.14451556
> 3.75043199
> H -2.28587949 -1.10947653
> 1.39188947
> H 3.27545810 0.69692463
> -2.80424123
> H 1.32239784 1.84191837
> 1.24408438
> H 0.04786402 -2.21233424
> 0.44588886
> H -3.33167216 3.06324516
> -0.45361872
> H -1.46660196 -0.18113393
> -1.30194026
> H -3.11195902 0.68820163
> 3.79014402
> H -3.17002906 -0.28179700
> -1.82562060
> H -3.36528818 2.07812052
> -1.93296467
> H -1.80366818 2.56266083
> -1.22199021
> H -2.64445872 -1.10184553
> -0.33379964
> H 3.54198727 -1.65065788
> 4.47432502
> H 4.66886299 -0.63426623
> -4.66333643
> H 3.17581803 0.06355822
> 4.72522318
> C -0.14571711 -0.19364594
> 2.18491398
> C 0.62275339 -0.19364594
> 0.98364221
> C -2.72522077 -0.20410595
> 3.29237670
> C -2.51079563 -0.19933695
> -0.95169504
> C 2.12817336 -0.20570595
> -1.35939330
> ...
> 90
>
> H...
>
> Eric
> --- "B. Bennion" <bbennion_at_u.washington.edu> wrote:
> > Hi Eric,
> >
> > Do you have babel installed (correctly)?
> > VMD uses this program to read in atoms in a
> > multitude of different
> > formats. There are several xyz formats and babel
> > will recognize them if
> > installed properly.
> >
> > Brian
> >
> >
> > On Thu, 10 Oct 2002, eric hu wrote:
> >
> > > Date: Thu, 10 Oct 2002 15:57:13 -0700 (PDT)
> > > From: eric hu <erichu_linux_at_yahoo.com>
> > > To: vmd-l_at_ks.uiuc.edu
> > > Subject: molden xyz movie
> > >
> > > Hi, I generated a xyz format movie with molden.
> > VMD
> > > does not seem to read it. I wonder if this is the
> > same
> > > xyz format that vmd requires or I need to do some
> > > modifications. Thanks.
> > >
> > > Best,
> > > -Yunfeng
> > >
> > >
> > >
> > > __________________________________________________
> > > Do you Yahoo!?
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> > >
> >
> >
> >
> >
> > Graduate Research Assistant
> > Dep. Medicinal Chemistry, University of Washington
> > Tel# (206)616-2779
> > BOX 357610 Seattle WA 98195
> >
> > email--bbennion_at_u.washington.edu
> > web page--http://students.washington.edu/bbennion
> >
>
>
> __________________________________________________
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> Faith Hill - Exclusive Performances, Videos & More
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>

Graduate Research Assistant
Dep. Medicinal Chemistry, University of Washington
Tel# (206)616-2779
BOX 357610 Seattle WA 98195

email--bbennion_at_u.washington.edu
web page--http://students.washington.edu/bbennion