VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_vitae.cmm.upenn.edu)
Date: Mon Oct 17 2005 - 19:37:14 CDT

On Mon, 17 Oct 2005, John Stone wrote:

hi john and stan,

the attached piece of code might help you.
i've written that long ago for a specific project so they
could get their trajectories into VMD by creating a
pdb + dcd file.
it should be pretty generic enough (and if not, easily adaptable).

good luck,
     axel.

JS>
JS> Stan,
JS> I encountered the same error when I tried loading your g96 file,
JS> I'll take a closer look at this problem and let you know what I find out.

JS>
JS> John Stone
JS> vmd_at_ks.uiuc.edu
JS>
JS> On Mon, Oct 17, 2005 at 05:26:17PM -0400, Stanley Lan wrote:
JS> > Hello everyone,
JS> >
JS> > I am trying to make a movie by using the initial coordinate file and the
JS> > trajectory file from GROMOS96 simulation result.
JS> >
JS> > Loading the coordinate file was not a problem but I couldn't load the
JS> > trajectory file by selecting the g96 format. VMD showed the following
JS> > error msg:
JS> > "No Structure information in file /<path>/<trajectory file>"
JS> > "ERROR) Could not read file /<path>/<trajectory file>"
JS> >
JS> > If I selected any other available formats, VMD simply showed me:
JS> > "ERROR) Could not read file /<path>/<trajectory file>"
JS> >
JS> > Is there a way to "turn up" the log level so that the error message can be
JS> > more interpretable and verbose?
JS> >
JS> > I am using VMD 1.8.3 on a linux PC (slackware10.2)
JS> >
JS> > My final goal is to make a movie out of my initial coordinates and the
JS> > trajectory from GROMOS result.
JS> >
JS> > Thanks in advance.
JS> >
JS> > -Stanley
JS> >
JS> > Here is part of my trajectory file (I deleted a big portion of it since
JS> > they didn't seem important to me, I could be wrong. Please contact me if
JS> > you need the complete file for testing.):
JS> >
JS> > =BOF=
JS> > TITLE
JS> > $Id: iempcl.dat,v 1.2 2000/10/20 12:29:39 gromos Exp $
JS> > END
JS> > TIMESTEP
JS> > 147 0.518588722
JS> > END
JS> > ENERGY
JS> > # ENER
JS> > -0.3215475E+05
JS> > 0.7724562E+04
JS> > 0.7724562E+04
JS> > 0.2910733E+02
JS> > 0.2910733E+02
JS> > 0.2910733E+02
JS> > 0.7695455E+04
JS> > 0.7695455E+04
JS> > -0.3987932E+05
JS> > 0.0000000E+00
JS> > # 10
JS> > 0.0000000E+00
JS> > 0.0000000E+00
JS> > 0.2553529E+02
JS> > 0.0000000E+00
JS> > 0.0000000E+00
JS> > 0.0000000E+00
JS> > 0.0000000E+00
JS> > 0.6098352E+04
JS> > -0.4648930E+05
JS> > -0.3175785E+03
JS> > # 20
JS> > 0.8036724E+03
JS> > 0.0000000E+00
JS> > # ENERES
JS> > 0.0000000E+00
JS> > 0.0000000E+00
JS> > 0.0000000E+00
JS> > 0.0000000E+00
JS> > 0.0000000E+00
JS> > 0.0000000E+00
JS> > # NUMUSD
JS> > 3
JS> > # ENERLJ,ENERCL,ENERRF,ENERRC
JS> > 0.4619526E+01 0.3951470E+03 -0.6761563E+02 0.6620401E+02
JS> > 0.5665094E+02 -0.2613196E+04 0.2889851E+02 0.7374684E+03
JS> > -0.1190074E+03 -0.9500724E+03 0.1531307E+03 0.1461857E-04
JS> > -0.2879240E+00 0.1225865E+03 -0.2392660E+02 0.0000000E+00
JS> > 0.7889620E+02 -0.8599962E+03 -0.1382724E+03 0.4296198E-06
JS> > 0.6077481E+04 -0.4258377E+05 -0.2697931E+03 -0.5871092E-05
JS> > END
JS> > POSITIONRED
JS> > 1.126477718 1.364905596 1.582740545
JS> > 1.274110794 1.436378002 1.588123560
JS> > 1.196202159 1.413280845 1.529842257
JS> > 1.150310636 1.494140029 1.493021369
JS> > 1.237280846 1.322410583 1.421857595
JS> > 1.116110444 1.268722653 1.345409513
JS> > 1.041743159 1.369518042 1.257558942
JS> > 1.157806635 1.148080349 1.261076927
JS> > 1.335683942 1.393326402 1.328620553
JS> > 1.447785378 1.344178796 1.316570878
JS> > # 10
JS> > 1.297751665 1.514312387 1.288480163
JS> > 1.203242421 1.546259999 1.295231819
JS> > [Deleted]
JS> > 2.443255663 2.409054279 2.123311281
JS> > 2.324791193 2.998526096 1.911451221
JS> > # 2830
JS> > 2.352324724 2.907167435 1.881488562
JS> > 2.311476469 2.996967316 2.010550261
JS> > 1.946586013 2.790724039 2.087211609
JS> > 1.871105909 2.766450882 2.025480032
JS> > 2.012133360 2.714556694 2.089403629
JS> > 2.275995493 2.807771683 2.853367329
JS> > 2.291668892 2.787541151 2.756246328
JS> > 2.206549168 2.744504929 2.888798475
JS> > END
JS> > BOX
JS> > 3.045200109 3.058700085 3.006109953
JS> > END
JS> > =EOF=
JS> >
JS>
JS> 

-- 
=======================================================================
Axel Kohlmeyer    e-mail: akohlmey_at_cmm.upenn.edu, tel: ++1-215-898-1582
Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.