[gmx-users] error coordinates in .gro donnot match .top

[Justin A. Lemkul]

Asmaa Elsheshiny wrote:
> Hi, all
> when I want to use gromacs preprocessor grompp to obtain  .tpr to use in the energy minimization as follow
>  grompp -f minim.mdp -c bradywaterbox.gro -p brady.top -o minimbrady.tpr
> 
> I got the following error message
> Fatal error:
> number of coordinates in coordinate file (bradywaterbox.gro, 670)
>              does not match topology (brady.top, 0)
> 
> 
> where,  bradywaterbox.gro & brady.top are obtained from 
> genbox -cp solvatedbrady.gro -cs spc216.gro -o bradywaterbox.gro -p brady.top
> 
> I think that the topology file didnot include the solvent molecules so it canont be mached with the coordinate file .gro , did it?
> So how can I fix this problem?
> 

There is a section regarding this error here:

http://www.gromacs.org/Documentation/Errors

grompp doesn't seem to think your topology has anything in it at all, so it's 
not simply an issue of the waters.

-Justin

> Regards,
> Asmaa 
> 
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-- 
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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

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