Jack Shultz wrote:
If I preped the tpr using amber forcefields, could that be the reason?
No.
The mdrun I am using does not have any force field libraries in its
directory.
That's irrelevant. Only non-mdrun tools care about the contents of
$GMXLIB or local force field files. The point of GROMPP is that it is
the GROMacs Pre-Processor that does all such for mdrun.
When you get some advice, it's good politics to be seen to follow those
up (or reject with reasons) before casting about wildly with other
theories :-) You don't want the people giving free advice feeling like
you're wasting their time!
Mark
On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham <[email protected]> wrote:
Jack Shultz wrote:
I preped this ligand using acpypi followed by grompp
grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top
I tested this .tpr file on my server. WheI had another computer run it
I get the following message. However we are using the same versions of
gromacs.
Back Off! I just backed up md.log to ./#md.log.2#
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: tpxio.c, line: 1643
Fatal error:
Can not read file topol.tpr,
this file is from a Gromacs version which is older than 2.0
Make a new one with grompp or use a gro or pdb file, if
possible
-------------------------------------------------------
I'd say it's evident that if the file is not corrupted (use gmxcheck), the
GROMACS installations weren't the same (unmodified) version. Reproduce the
conditions and run grompp -h to inspect the version.
Perhaps you are having a problem with a shared-library mismatch.
If you have such an old version of GROMACS around, either uninstall it and
retire the sysadmin, or send the computer to a museum :-)
Mark
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