[gmx-users] Atoms in the .top are not numbered consecutively from 1

[Justin A. Lemkul]

sreelakshmi ramesh wrote:
> Dear all,
>             when i run energy minimization  i get the following error.
> 
> the topology file was created from the starting pdb file using g_x2top
> 
> *grompp  -f em.mdp  -c out.gro -p carbon.top  -o o.tpr -maxwarn 3*

In general, the use of -maxwarn is discouraged.  If grompp fails, then likely 
your simulation would too.  Using -maxwarn usually just allows you to bypass 
critical errors and wind up with a simulation that goes nowhere.

> Atoms in the .top are not numbered consecutively from 1 (rather, atomnr 
> = 348, while at->nr = 0)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 

This is a fairly straightforward error message.  Your atoms aren't numbered 
starting with 1, and they need to be.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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