[gmx-users] Error message in reading AMBER's mdcrd files?

[Justin A. Lemkul]

a a wrote:
> Dear Sir/Madam,
> 
> I have problem to read in mdcrd files.
> 
> I followed the procedures in the manual to 
> 
> (1) installed VERSION 4.5.5 gromacs
> 
> (2) installed VMD 
> 
> (3) in the .bashrc file, I added a line
> 
> export VMD_PLUGIN_PATH=/home/vmd_ied/lib/vmd/plugins/LINUX/molfile
> 
> (4) In the above molfile, I got all these so files:
> 
> avsplugin.so       dtrplugin.so      msmsplugin.so      tinkerplugin.so
> babelplugin.so     dxplugin.so       namdbinplugin.so   uhbdplugin.so
> basissetplugin.so  edmplugin.so      netcdfplugin.so    vaspchgcarplugin.so
> bgfplugin.so       fs4plugin.so      parm7plugin.so     va! s 
> poutcarplugin.so
> binposplugin.so    gamessplugin.so   parmplugin.so      vaspparchgplugin.so
> biomoccaplugin.so  graspplugin.so    pbeqplugin.so      vaspposcarplugin.so
> brixplugin.so      grdplugin.so      pdbplugin.so       vaspxdatcarplugin.so
> carplugin.so       gridplugin.so     phiplugin.so       vaspxmlplugin.so
> ccp4plugin.so      gromacsplugin.so  pltplugin.so       vtfplugin.so
> corplugin.so       jsplugin.so       pqrplugin.so       webpdbplugin.so
> cpmdplugin.so      lammpsplugin.so   psfplugin.so       xbgfplugin.so
> crdplugin.so       maeffplugin.so    raster3dplugin.so  xsfplugin.so
> cubeplug! in .so      mapplugin.so      rst7plugin.so      xyzplugin.so
> dcdplugin.so       mdfplugin.so      situsplugin.so
> dlpolyplugin.so    mol2plugin.so     spiderplugin.so
> dsn6plugin.so      moldenplugin.so   stlplugin.so
> 
> (5) I tested if I could run the gromacs as follows:
> 
> /usr/local/gromacs/bin/g_covar_d -s test.pdb -f test.mdcrd -o -v
> 
> (6) However, the following error message appeared.
> 
> ==================================================
> Program g_covar_d, VERSION 4.5.5
> Source code file: trxio.c, line: 870
> 
> Fatal error:
> Not supported in read_first_frame: test.mdcrd
> For more information and tips for troubleshooting, please check the GROMACS
> websit! e a t http://www.gromacs.org/Documentation/Errors
> ==================================================
> 
> Please kindly instruct if I have done anything wrong here.  Many thanks.
> 

I have never made use of this feature myself, but it seems to me that you have 
to install VMD first, then when configuring Gromacs, you need to invoke the 
--with-dlopen option during configuration.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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