[gmx-users] tpr older version message

Justin A. Lemkul jalemkul at vt.edu
Mon Dec 28 02:48:06 CET 2009



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 <Mark.Abraham at anu.edu.au> 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 <Mark.Abraham at anu.edu.au>
>>> 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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>>>
>>>
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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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