VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Mon Oct 24 2005 - 07:00:04 CDT

Hi Guys,

I'm having trouble with a piece of code that I thought was working. I need
to load two separate molecules and then align them structurally.

It goes something like this:

> mol load pdb prot-pitch-0.pdb
> set preprot [atomselect 0 "not water and not hydrogen"]
> $preprot writepdb inputp.pdb
> 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

This is all fine and well for the first protein. However, when further down
in the code I issue 'resetpsf', read in another molecule, and do the same
operation, I find that I cannot write out the second molecule. The writepdb
command insists on writing out the first molecule! Thus it seems that even
with resetpsf, the first molecule is in memory and the second molecule is
just ignored. Maybe issuing resetpsf is not enough to clarify which
molecule should be written out by the writepdb command. At any rate, could
you advise as to correct procedure for this?

Many thanks,

Sam

> ..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=
>
>