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

[Justin A. Lemkul]

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: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > 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

========================================