VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Mon Oct 24 2005 - 11:15:22 CDT

Sam,

   You probably need to specify the selection when writing out the
second PDB file.

$selection writepdb x.pdb

Set "selection" wrt the molecule number (set selection [atomselect
molnum "selection_text"]), and writepdb should work fine, I think.

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Samuel Flores
> Sent: Monday, October 24, 2005 6:00 AM
> To: 'JC Gumbart'
> Cc: vmd-l_at_ks.uiuc.edu; 'Stanley Lan'
> Subject: vmd-l: problem with writepdb
>
> 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=
> >
> >
>
>
>