VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Oct 17 2005 - 19:25:49 CDT

Try typing resetpsf between the two proteins.

On Oct 17, 2005, at 7:16 PM, Samuel Flores wrote:

>
> 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=
>
>