[gmx-users] Grompp error

fsaadedi at staffmail.ed.ac.uk fsaadedi at staffmail.ed.ac.uk
Sat Dec 3 03:37:42 CET 2005

Dear Alan and Mark,

Thank you for your advice, I have managed to fix the particular problem 
by sorting out the top and pdb file.


Farid Sa'adedin

Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:

> Farid Sa'adedin wrote:
>> Dear Users,
>> I have added Cl ion to my peptide in water system pdb and topology files.
>> But I have a problem when I run grompp:
>> Fatal Error: Atoms in the .top are not numbered consecutively from 1.
>> The pdb is numbered correctly and I have added the the spc.itp and 
>> clion.itp to the topology file.
> I would have a look at the .top file and see how the atoms are not
> numbered consecutively from 1, and do something appropriate about it.
> Perhaps you should use genbox to add chloride and water before using
> pdb2gmx to generate your .top file.
> Mark
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list