[gmx-users] pairing error

[Justin A. Lemkul]

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>> 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> | (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

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