a a wrote:
Hi Justin ,
Could you tell me what is --with--dlopen option during configuration?
Invoking --with-dlopen enables the optional VMD-reading capabilities.
Do you mean it is a command that I should have used when I install
GROMACS? I am new to GROMACS, please kindly let me know more details
about the steps/commands that I should use the mentioned option?
Simply add --with-dlopen to your ./configure command.
-Justin
Best regards,
Cat
> 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.
>
> -
> Date: Sun, 8 Apr 2012 12:25:31 -0400
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] Error message in reading AMBER's mdcrd files?
>
>
>
> 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
> &! gt; 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/groma! cs/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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--
========================================
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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