[gmx-users] tpr older version message

[Jack Shultz]

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
-------------------------------------------------------



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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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org