[gmx-users] Grompp error

[fsaadedi at staffmail.ed.ac.uk]

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.

Yours

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
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