VMD-L Mailing List

From: Tru Huynh (tru_at_pasteur.fr)
Date: Wed Dec 09 2009 - 13:37:45 CST

On Tue, Dec 08, 2009 at 02:44:06PM -0600, John Stone wrote:
>
> Hi,
> What happens if you do this:
> package require psfgen
>
[tru_at_liberte ~]$ module load vmd/1.8.7-local
[tru_at_liberte ~]$ vmd
Info) VMD for LINUXAMD64, version 1.8.7 (December 2, 2009)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info) Free system memory: 23224MB (96%)
XRequest.145: BadRequest (invalid request code or no such operation) 0x2400046
XRequest.145: BadRequest (invalid request code or no such operation) 0x2400046
XRequest.145: BadRequest (invalid request code or no such operation) 0x2400046
Info) OpenGL renderer: GeForce FX 5200/AGP/SSE2
Info) Features: STENCIL MDE MTX PP PS
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
The irspecgui package could not be loaded:

The multiseq package could not be loaded:

The pmepot_gui package could not be loaded:

The solvate package could not be loaded:

The autopsf package could not be loaded:

The cggui package could not be loaded:

The dowser_gui package could not be loaded:

The membrane package could not be loaded:

The mutator package could not be loaded:

The autoimd package could not be loaded:

vmd > package require psfgen
can't find package psfgen

> Do you get an error, or does that succeed?
>
> Within your plugin builds, do you find the following compiled
> shared object files?:
> vmd188a5/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so
> vmd188a5/plugins/LINUX/tcl/hesstrans1.0/hesstrans.so
> vmd188a5/plugins/LINUX/tcl/libbiokit1.1/tcl_libbiokit.so
> vmd188a5/plugins/LINUX/tcl/signalproc1.1/sgsmooth.so
> vmd188a5/plugins/LINUX/tcl/signalproc1.1/specden.so
> vmd188a5/plugins/LINUX/tcl/signalproc1.1/fftcmds.so
> vmd188a5/plugins/LINUX/tcl/autopsf1.2/psfcheck.so
> vmd188a5/plugins/LINUX/tcl/mutator1.2/libalchemify.so
> vmd188a5/plugins/LINUX/tcl/pmepot1.0/libpmepot.so
> vmd188a5/plugins/LINUX/tcl/psfgen1.4/libpsfgen.so
no: most of the .so files are in plugins/LINUXAMD64/molfile:

[tru_at_liberte 1.8.7]$ find plugins -name \*.so
plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so
plugins/LINUXAMD64/molfile/graspplugin.so
plugins/LINUXAMD64/molfile/gromacsplugin.so
plugins/LINUXAMD64/molfile/vaspxmlplugin.so
plugins/LINUXAMD64/molfile/raster3dplugin.so
plugins/LINUXAMD64/molfile/pdbplugin.so
plugins/LINUXAMD64/molfile/grdplugin.so
plugins/LINUXAMD64/molfile/carplugin.so
plugins/LINUXAMD64/molfile/jsplugin.so
plugins/LINUXAMD64/molfile/xyzplugin.so
plugins/LINUXAMD64/molfile/vaspchgcarplugin.so
plugins/LINUXAMD64/molfile/dcdplugin.so
plugins/LINUXAMD64/molfile/dlpolyplugin.so
plugins/LINUXAMD64/molfile/vaspoutcarplugin.so
plugins/LINUXAMD64/molfile/situsplugin.so
plugins/LINUXAMD64/molfile/xbgfplugin.so
plugins/LINUXAMD64/molfile/spiderplugin.so
plugins/LINUXAMD64/molfile/maeffplugin.so
plugins/LINUXAMD64/molfile/biomoccaplugin.so
plugins/LINUXAMD64/molfile/parmplugin.so
plugins/LINUXAMD64/molfile/corplugin.so
plugins/LINUXAMD64/molfile/vaspxdatcarplugin.so
plugins/LINUXAMD64/molfile/psfplugin.so
plugins/LINUXAMD64/molfile/binposplugin.so
plugins/LINUXAMD64/molfile/namdbinplugin.so
plugins/LINUXAMD64/molfile/uhbdplugin.so
plugins/LINUXAMD64/molfile/stlplugin.so
plugins/LINUXAMD64/molfile/bgfplugin.so
plugins/LINUXAMD64/molfile/fs4plugin.so
plugins/LINUXAMD64/molfile/pltplugin.so
plugins/LINUXAMD64/molfile/edmplugin.so
plugins/LINUXAMD64/molfile/vtfplugin.so
plugins/LINUXAMD64/molfile/moldenplugin.so
plugins/LINUXAMD64/molfile/gamessplugin.so
plugins/LINUXAMD64/molfile/dxplugin.so
plugins/LINUXAMD64/molfile/crdplugin.so
plugins/LINUXAMD64/molfile/parm7plugin.so
plugins/LINUXAMD64/molfile/basissetplugin.so
plugins/LINUXAMD64/molfile/avsplugin.so
plugins/LINUXAMD64/molfile/mol2plugin.so
plugins/LINUXAMD64/molfile/dtrplugin.so
plugins/LINUXAMD64/molfile/phiplugin.so
plugins/LINUXAMD64/molfile/tinkerplugin.so
plugins/LINUXAMD64/molfile/vaspposcarplugin.so
plugins/LINUXAMD64/molfile/vaspparchgplugin.so
plugins/LINUXAMD64/molfile/babelplugin.so
plugins/LINUXAMD64/molfile/cubeplugin.so
plugins/LINUXAMD64/molfile/xsfplugin.so
plugins/LINUXAMD64/molfile/dsn6plugin.so
plugins/LINUXAMD64/molfile/ccp4plugin.so
plugins/LINUXAMD64/molfile/gridplugin.so
plugins/LINUXAMD64/molfile/cpmdplugin.so
plugins/LINUXAMD64/molfile/mapplugin.so
plugins/LINUXAMD64/molfile/msmsplugin.so
plugins/LINUXAMD64/molfile/mdfplugin.so
plugins/LINUXAMD64/molfile/rst7plugin.so
plugins/LINUXAMD64/molfile/pbeqplugin.so
plugins/LINUXAMD64/molfile/brixplugin.so
plugins/LINUXAMD64/molfile/lammpsplugin.so
plugins/LINUXAMD64/molfile/pqrplugin.so
plugins/LINUXAMD64/tcl/hesstrans1.0/hesstrans.so

So the plugins tree is definitely missing quite a lot of .so files :(

> Also, for completeness, can you show me the top couple of
> levels of the directory structure of your VMD installation?
> I would expect to see something that looks almost exactly like this:
>
> johns_at_casablanca.ks.uiuc.edu{335} ls vmd188a5
> Announcement LICENSE scripts surf_LINUX vmd_LINUX
> doc plugins shaders tachyon_LINUX
> libcudart.so.2 README stride_LINUX vmd_completion.dat
[tru_at_liberte 1.8.7]$ pwd
/c5/shared/vmd/local/1.8.7
[tru_at_liberte 1.8.7]$ ls
Announcement README stride_LINUXAMD64* vmd-1.8.7*
doc/ scripts/ surf_LINUXAMD64* vmd_completion.dat
LICENSE shaders/ tachyon_LINUXAMD64@ vmd_LINUXAMD64*
plugins/ stride@ vmd*

>
> johns_at_casablanca.ks.uiuc.edu{336} ls vmd188a5/plugins/
> include LINUX noarch
>
[tru_at_liberte 1.8.7]$ ls plugins/
include/ LINUX/ LINUXAMD64/ noarch/ WIN32/

> johns_at_casablanca.ks.uiuc.edu{337} ls vmd188a5/plugins/noarch/tcl
> apbsrun1.3 hbonds1.1 namdserver1.1 runante0.1
> atomedit1.0 idatm0.1 nanotube1.0 saltbr1.0
> autoimd1.6 ilstools1.2 navfly1.0 seqdata1.1
> autoionize1.2 ilstools1.3 navigate1.0 seqedit1.1
> bignum1.0 imdmenu1.0 optimization1.0 solvate1.3
> biocore1.1 inorganicbuilder0.1 palettetool1.0 ssrestraints1.0
> blast1.1 irspecgui1.1 paratool1.4 stingtool1.0
> cgtools1.0 mdff0.2 pbctools2.5 symmetrytool1.2
> cliptool1.0 membrane1.0 pdbtool1.0 symmetrytool1.3
> clonerep1.1 mergestructs1.0 phylotree1.1 timeline2.0
> colorscalebar1.2 molefacture1.1 psipred1.1 topotools1.0
> colorscalebar1.3 moltoptools0.1 qmtool1.1 topotools1.1
> contactmap1.1 multimolanim1.0 ramaplot1.1 trunctraj1.5
> dataimport1.0 multiplot1.4 readcharmmpar1.1 utilities1.0
> demomaster1.0 multiseq2.1 readcharmmtop1.0 vdna2.0
> dipwatch1.2 multiseqdialog1.1 resptool1.1 viewmaster2.2
> dowser1.0 multitext1.0 rmsd1.0 vmdmovie1.7
> exectool1.2 namdenergy1.2 rmsdtt2.0 vmdtkcon1.1
> extendedpdb1.0 namdgui1.2 rnaview1.0 volmapgui1.1
> gofrgui1.1 namdplot1.0 ruler1.0 zoomseq1.1
>
[tru_at_liberte 1.8.7]$ ls plugins/noarch/tcl/
apbsrun1.3/ hbonds1.1/ nanotube1.0/ runante0.1/
atomedit1.0/ idatm0.1/ navfly1.0/ saltbr1.0/
autoimd1.6/ ilstools1.2/ navigate1.0/ seqdata1.1/
autoionize1.2/ imdmenu1.0/ optimization1.0/ seqedit1.1/
bignum1.0/ inorganicbuilder0.1/ palettetool1.0/ solvate1.3/
biocore1.1/ irspecgui1.1/ paratool1.4/ ssrestraints1.0/
blast1.1/ membrane1.0/ pbctools2.5/ stingtool1.0/
cgtools1.0/ mergestructs1.0/ pdbtool1.0/ symmetrytool1.2/
cliptool1.0/ molefacture1.1/ phylotree1.1/ timeline2.0/
clonerep1.1/ moltoptools0.1/ psipred1.1/ topotools1.0/
colorscalebar1.2/ multimolanim1.0/ qmtool1.1/ trunctraj1.5/
contactmap1.1/ multiplot1.4/ ramaplot1.1/ utilities1.0/
dataimport1.0/ multiseq2.1/ readcharmmpar1.1/ vdna2.0/
demomaster1.0/ multiseqdialog1.1/ readcharmmtop1.0/ viewmaster2.2/
dipwatch1.2/ multitext1.0/ resptool1.1/ vmdmovie1.7/
dowser1.0/ namdenergy1.2/ rmsd1.0/ vmdtkcon1.1/
exectool1.2/ namdgui1.2/ rmsdtt2.0/ volmapgui1.1/
extendedpdb1.0/ namdplot1.0/ rnaview1.0/ zoomseq1.1/
gofrgui1.1/ namdserver1.1/ ruler1.0/

Thanks

Tru 

-- 
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru_at_pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France