[gmx-users] pairing error
mohit kumar
sahajmohit at gmail.com
Mon Aug 10 18:03:05 CEST 2009
im using dell core 2 duo with linux mint
On Mon, Aug 10, 2009 at 10:37 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> mohit kumar wrote:
>
>> still im getting problem, i checked the funct its have numerical
>> value..stilll getting problem..do i have to install gromac 3 version for
>> that..coz i having 4.0.5 version...
>>
>>
> Working with the most recent version (4.0.5) is always recommended. The
> only reason to use an old version would be for consistency with older work.
> Can you post your [ pairs ] section so we can have a look? What type of
> machine are you using? If it's Windows, then there may be problems with the
> file if it was edited using anything other than a plain text editor, in
> which case dos2unix is your friend.
>
> -Justin
>
> On Thu, Aug 6, 2009 at 3:22 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> mohit kumar wrote:
>>
>> but i dnt find any 'type' column in my topology file..the grompp
>> programm with this top file works gud in 3.3 version..im having
>> 4.0.5 version..is that can be issue?? shud i try in 3.3 version
>>
>>
>> This may be some new error-checking mechanism introduced in version
>> 4.0. In your topology, a function type for pairs should be defined,
>> according to the header of this section (from pdb2gmx):
>>
>> [ pairs ]
>> ; ai aj funct c0 c1 c2
>> c3
>>
>> If your "funct" column is blank or says "0" then that could be
>> giving the error.
>>
>> -Justin
>>
>> On Thu, Aug 6, 2009 at 2:48 PM, Justin A. Lemkul
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>> mohit kumar wrote:
>>
>> im running energy minimization for POPC bilayer but its
>> showing
>> error which i cant figure out
>>
>> -- -------------------------------------------------------
>> Program grompp, VERSION 4.0.5
>> Source code file: topdirs.c, line: 99
>>
>> Fatal error:
>> Invalid pairs type 0
>>
>> what does this pair type mean and how can i solve it??
>> plz help me
>>
>>
>> The error message is pretty clear. Somewhere within the
>> topology,
>> you have a "0" in the "type" column, which doesn't correspond
>> to any
>> known pair type.
>>
>> -Justin
>>
>>
>>
>> MOHIT KUMAR
>> Molecular Biochemistry & Biophysics
>> Graduate Student
>> Illinois Institute of Technology
>> Chicago,IL, USA
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>> 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
>>
>> -- MOHIT KUMAR
>> Molecular Biochemistry & Biophysics
>> Graduate Student
>> Illinois Institute of Technology
>> Chicago,IL, USA
>>
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>>
>>
>>
>> --
>> MOHIT KUMAR
>> Molecular Biochemistry & Biophysics
>> Graduate Student
>> Illinois Institute of Technology
>> Chicago,IL, USA
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>
--
MOHIT KUMAR
Molecular Biochemistry & Biophysics
Graduate Student
Illinois Institute of Technology
Chicago,IL, USA
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