Jack Shultz wrote:
Hi Marc,
I figured it out. I tried upir suggestion and tested the gmxcheck but
got the following errors
gmxcheck.exe -s1 topol.tpr
Please give me TWO run input (.tpr/.tpa/.tpb) files
or specify the -m flag to generate a methods.tex file
gmxcheck.exe -s1 topol.tpr -m
-------------------------------------------------------
Program gmxcheck, 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
-------------------------------------------------------
gmxcheck -c is the appropriate usage for checking the contents of a single .tpr
file. Using -s1 implies -s2, per the documentation.
-Justin
gcq#332: Thanx for Using GROMACS - Have a Nice Day
But then decided I need to run the grompp on my clients along with the
pre-processing libraries generated by acpypi. Then tested the mdrun on
the .tpr this generated. Then it was missing the aminoacids.dat I
downloaded it and everything seems to work. I will now make some
additional steps on this workflow so this should now work!
Thanks again for your help I very much appreciate it.
On Sun, Dec 27, 2009 at 7:18 PM, Mark Abraham <[email protected]> wrote:
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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--
========================================
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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