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
--
========================================
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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