[gmx-users] Re: trjconv error

[parthiban at ncbs.res.in]

> 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
>>> -------------------------------------------------------