VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Mon Oct 17 2005 - 19:16:33 CDT

Hi Guys,

I wonder if I could have some advice on a problem I'm having. I want to
load two molecules, then align them structurally. I used some of the code
from the NAMD tutorial to load the first molecule:

mol load pdb prot-pitch-0.pdb
set preprot [atomselect 0 "not water and not hydrogen"]
$preprot writepdb inputp.pdb
# ubq.pgn, namd tutorial
package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment U {pdb inputp.pdb}
coordpdb inputp.pdb U
guesscoord
writepdb input.2.pdb
writepsf input.2.psf

        ..And this was successful. Then I went to load the second protein:

mol load pdb input.pdb
set inputprot [atomselect 2 "not water and not hydrogen"]
$inputprot writepdb inputprotp.pdb
segment IU {pdb inputprotp.pdb}
coordpdb inputprotp.pdb IU
guesscoord
writepdb inputprot.2.pdb
writepsf inputprot.2.psf

        When I look at inputprot.2.pdb, it has TWO copies of the protein --
the first and the second! The first gets its coordinates zeroed out,
depending on whether guesscoord is used or not.

Since the second protein loaded has twice the expected number of atoms, it
is impossible to do a structural alignment. And yet I have to do the whole
coordpdb and guesscoord thing because otherwise it misidentifies some of the
atoms. Obviously when it goes through coordpdb, guesscoord, writepdb, etc.
the second time around, it still has the coordinates of the first protein in
memory. Can anyone tell me how to flush the first protein out of memory, or
in some way deal with this issue?

Thanks

Sam

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Stanley Lan
Sent: Monday, October 17, 2005 5:26 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Cannot load Gromos96 trajectory file (attached)

Hello everyone,

I am trying to make a movie by using the initial coordinate file and the
trajectory file from GROMOS96 simulation result.

Loading the coordinate file was not a problem but I couldn't load the
trajectory file by selecting the g96 format. VMD showed the following error

msg:
"No Structure information in file /<path>/<trajectory file>"
"ERROR) Could not read file /<path>/<trajectory file>"

If I selected any other available formats, VMD simply showed me:
"ERROR) Could not read file /<path>/<trajectory file>"

Is there a way to "turn up" the log level so that the error message can be
more interpretable and verbose?

I am using VMD 1.8.3 on a linux PC (slackware10.2)

My final goal is to make a movie out of my initial coordinates and the
trajectory from GROMOS result.

Thanks in advance.

-Stanley

Here is part of my trajectory file (I deleted a big portion of it since they

didn't seem important to me, I could be wrong. Please contact me if you
need the complete file for testing.):

=BOF=
TITLE
$Id: iempcl.dat,v 1.2 2000/10/20 12:29:39 gromos Exp $
END
TIMESTEP
            147 0.518588722
END
ENERGY
# ENER
-0.3215475E+05
  0.7724562E+04
  0.7724562E+04
  0.2910733E+02
  0.2910733E+02
  0.2910733E+02
  0.7695455E+04
  0.7695455E+04
-0.3987932E+05
  0.0000000E+00
# 10
  0.0000000E+00
  0.0000000E+00
  0.2553529E+02
  0.0000000E+00
  0.0000000E+00
  0.0000000E+00
  0.0000000E+00
  0.6098352E+04
-0.4648930E+05
-0.3175785E+03
# 20
  0.8036724E+03
  0.0000000E+00
# ENERES
  0.0000000E+00
  0.0000000E+00
  0.0000000E+00
  0.0000000E+00
  0.0000000E+00
  0.0000000E+00
# NUMUSD
    3
# ENERLJ,ENERCL,ENERRF,ENERRC
  0.4619526E+01 0.3951470E+03 -0.6761563E+02 0.6620401E+02
  0.5665094E+02 -0.2613196E+04 0.2889851E+02 0.7374684E+03
-0.1190074E+03 -0.9500724E+03 0.1531307E+03 0.1461857E-04
-0.2879240E+00 0.1225865E+03 -0.2392660E+02 0.0000000E+00
  0.7889620E+02 -0.8599962E+03 -0.1382724E+03 0.4296198E-06
  0.6077481E+04 -0.4258377E+05 -0.2697931E+03 -0.5871092E-05
END
POSITIONRED
    1.126477718 1.364905596 1.582740545
    1.274110794 1.436378002 1.588123560
    1.196202159 1.413280845 1.529842257
    1.150310636 1.494140029 1.493021369
    1.237280846 1.322410583 1.421857595
    1.116110444 1.268722653 1.345409513
    1.041743159 1.369518042 1.257558942
    1.157806635 1.148080349 1.261076927
    1.335683942 1.393326402 1.328620553
    1.447785378 1.344178796 1.316570878
# 10
    1.297751665 1.514312387 1.288480163
    1.203242421 1.546259999 1.295231819
[Deleted]
   2.443255663 2.409054279 2.123311281
    2.324791193 2.998526096 1.911451221
# 2830
    2.352324724 2.907167435 1.881488562
    2.311476469 2.996967316 2.010550261
    1.946586013 2.790724039 2.087211609
    1.871105909 2.766450882 2.025480032
    2.012133360 2.714556694 2.089403629
    2.275995493 2.807771683 2.853367329
    2.291668892 2.787541151 2.756246328
    2.206549168 2.744504929 2.888798475
END
BOX
    3.045200109 3.058700085 3.006109953
END
=EOF=