[gmx-users] pairing error

[Justin A. Lemkul]

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
> 
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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

========================================