[gmx-users] Re: trjconv error

Thu Aug 28 10:02:12 CEST 2008

You seem not to get it... I specifically chew out for you that you
need to give a listing using the command ls -l. That will also show
what the size of the file is. This is completely pointless this way!
Also, you only now state the command you gave.

Now, rereading the first mail, it also said ..time 3.5, so it didn't
bail out directly as I thought initially, but read a few frames. Now
you'll probabaly go "right, suits you for not reading my mail
thoroughly", but that's not what this list is about. You want
something from us, so you'll have to facilitate. We read dozens and
dozens of mails, checking if we can give a hand or pointer somewhere,
so pardon us for scanning superficially. For instance, your first mail
would've been much clearer if you'd given the command as you used it
and the complete output of it. Also, get used to do as much as
possible yourself. Something wrong with a trajectory? Run gmxcheck,
that's what it's for. That gives you an error? Check the
archives/wiki. Is the size of the file consistent with a trajectory of
as many frames as you get? Bummer, trajectory corrupt, crash, harddisk
full, or something along those lines. You'll have to redo the
simulation. Are you sure there are more frames? You can track down
another post of mine from yesterday or the day before (keyword split).

I recall having already sent this link:
http://www.catb.org/~esr/faqs/smart-questions.html

But I don't find anything that gives me the impression that it has
been read. Please do, for your own benefit.

Regards,

Tsjerk

On Thu, Aug 28, 2008 at 6:08 AM,  <parthiban at ncbs.res.in> wrote:
>> Message: 2
>> Date: Wed, 27 Aug 2008 15:31:58 +0530 (IST)
>> From: parthiban at ncbs.res.in
>> Subject: [gmx-users] trjconv error
>> To: gmx-users at gromacs.org
>> Message-ID: <45197.192.168.1.1.1219831318.squirrel at mail.ncbs.res.in>
>> Content-Type: text/plain;charset=iso-8859-1
>>
>> Dear Tsjerk
>>
>> we have checked it., but of no use it giving some error.,
>> for your kind information, this "trjconv_mpi" command works for a protein
>> with a drug molecule, a protein moleclue, a dimer, etc..
>>
>> but it gives out error only for a dimer with  a drug complex., its really
>> a mystery., if i am making error in preperation also gromacs should give
>> error while executing, but it does not.
>>
>> any suggestions.
>>
>> Thanks
>> Parthi & Sundar
>> -----------------------------------------------------------------
>>
>>> Message: 3
>>> Date: Wed, 27 Aug 2008 09:53:02 +0200
>>> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>>> Subject: Re: [gmx-users] trjconv error
>>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>>> Message-ID:
>>>      <8ff898150808270053y68ecb5f0mdf004fa1295ec521 at mail.gmail.com>
>>> Content-Type: text/plain; charset=ISO-8859-1
>>>
>>> Hi Parthiban and Sundar,
>>>
>>> Did you check the .trr file with gmxcheck?
>>>
>>> By the way, is this still that same (faulty) trjconv of these
>>> sysadmins of yours who compiled it with gcc 4.x?
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>>
>>> On Wed, Aug 27, 2008 at 8:36 AM,  <parthiban at ncbs.res.in> wrote:
>>>> hi all
>>>>
>>>> i can able to get .trr file after running md for 10 hrs
>>>> but i cannot able to get the .trr to .xtc file which gives out the
>>>> following error. can anyone guess, what type of error is this, & how to
>>>> resolve it..
>>>>
>>>> Parthiban & Sundar
>>>>
>>>> ------------------------------------------------------- time    3.500
>>>> Program trjconv_mpi, VERSION 3.3.1
>>>> Source code file: trnio.c, line: 66
>>>>
>>>> File input/output error:
>>>> Can not determine precision of trn file
>>>> -------------------------------------------------------
>>>>
>>
>> Message: 4
>> Date: Wed, 27 Aug 2008 12:19:31 +0200
>> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>> Subject: Re: [gmx-users] trjconv error
>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Message-ID:
>>       <8ff898150808270319g98be0d3wdf21c2be850a1960 at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi,
>>
>>> we have checked it., but of no use it giving some error.,
>>> for your kind information, this "trjconv_mpi" command works for a
>>> protein
>>> with a drug molecule, a protein moleclue, a dimer, etc..
>>
>> So it's not trjconv_mpi, it's the trajectory that's wrong.
>> Could you give the directory listing? (ls -l)
>>
>> Tsjerk
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>>
>
> hi
> here i have given the list of my files
> --------------------------------------------------
> em.mdp
> list.txt
> md.mdp
> mdout.mdp
> #mdout.mdp.1#
> #mdout.mdp.2#
> #mdout.mdp.3#
> nic.itp
> nic.pdb
> output.xtc
> posre_A.itp
> posre_B.itp
> pr.mdp
> protein_box.pdb
> protein_em0.log
> protein_em10.log
> protein_em11.log
> protein_em12.log
> protein_em13.log
> protein_em14.log
> protein_em15.log
> protein_em16.log
> protein_em17.log
> protein_em18.log
> protein_em19.log
> protein_em1.log
> protein_em20.log
> protein_em21.log
> protein_em22.log
> protein_em23.log
> protein_em24.log
> protein_em25.log
> protein_em26.log
> protein_em27.log
> protein_em28.log
> protein_em29.log
> protein_em2.log
> protein_em30.log
> protein_em31.log
> protein_em3.log
> protein_em4.log
> protein_em5.log
> protein_em6.log
> protein_em7.log
> protein_em8.log
> protein_em9.log
> protein_em.edr
> protein_em.gro
> protein_em.tpr
> #protein_em.tpr.1#
> protein_em.trr
> protein_ion.log
> protein_ion.pdb
> protein_md0.log
> protein_md10.log
> protein_md11.log
> protein_md12.log
> protein_md13.log
> protein_md14.log
> protein_md15.log
> protein_md16.log
> protein_md17.log
> protein_md18.log
> protein_md19.log
> protein_md1.log
> protein_md20.log
> protein_md21.log
> protein_md22.log
> protein_md23.log
> protein_md24.log
> protein_md25.log
> protein_md26.log
> protein_md27.log
> protein_md28.log
> protein_md29.log
> protein_md2.log
> protein_md30.log
> protein_md31.log
> protein_md3.log
> protein_md4.log
> protein_md5.log
> protein_md6.log
> protein_md7.log
> protein_md8.log
> protein_md9.log
> protein_md.edr
> protein_md.gro
> protein_md.tpr
> protein_md.trr
> protein_out.pdb
> protein.pdb
> protein_pr0.log
> protein_pr10.log
> protein_pr11.log
> protein_pr12.log
> protein_pr13.log
> protein_pr14.log
> protein_pr15.log
> protein_pr16.log
> protein_pr17.log
> protein_pr18.log
> protein_pr19.log
> protein_pr1.log
> protein_pr20.log
> protein_pr21.log
> protein_pr22.log
> protein_pr23.log
> protein_pr24.log
> protein_pr25.log
> protein_pr26.log
> protein_pr27.log
> protein_pr28.log
> protein_pr29.log
> protein_pr2.log
> protein_pr30.log
> protein_pr31.log
> protein_pr3.log
> protein_pr4.log
> protein_pr5.log
> protein_pr6.log
> protein_pr7.log
> protein_pr8.log
> protein_pr9.log
> protein_pr.edr
> protein_pr.gro
> protein_pr.tpr
> protein_pr.trr
> protein_solv.pdb
> topology_A.itp
> topology_B.itp
> topology.top
> #topology.top.1#
> ----------------------------------------------------------
> any suggestions.,
>
> and the command which i gave for trjconv is
>
> trjconv_mpi -f protein_md.trr -o protein_final.xtc
>
> and the error is
>
>>>> ------------------------------------------------------- time    3.500
>>>> Program trjconv_mpi, VERSION 3.3.1
>>>> Source code file: trnio.c, line: 66
>>>>
>>>> File input/output error:
>>>> Can not determine precision of trn file
>>>> -------------------------------------------------------
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623