[gmx-users] Regarding error

[Mark Abraham]

On 4/06/2012 5:05 PM, Seera Suryanarayana wrote:
> Dear all gromacs users,
>
>                                   While i am running pdb2gmx commond i 
> am getting following error.
>
> Fatal error:
> There were 22 missing atoms in molecule Protein_chain_A, if you want 
> to use
> this incomplete topology.
>
> I wont ignore the 22 missing atoms by using -missing commond. I would 
> like to construct a complete protein structure.But i dont know how to 
> construct the complete protein sturcture.Kindly tell me how to 
> consturct the complete protein and what are the softwares i have to 
> use here.

There is no general answer to this question. You have to examine the 
file, see what is missing, perhaps find out why, and then perhaps use 
various possible solutions. Some leads are here... 
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File

Mark