[gmx-users] Error- Atom not found in residue seq nr while adding atom

[Mark Abraham]

On 18/04/12, aiswarya pawar <aiswarya.pawar at gmail.com> wrote:

>  Hi Users,
> 
> I did the following step=
>  pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top
> 
> 
> and received an error= Atom ND1 not found in residue seq.nr(http://seq.nr/). 7 while adding atom.
> 
> I dont understand how do i rectify this.
> 
  
You're telling pdb2gmx to ignore hydrogens in the input, so it's trying to add them back, but the residue it identifies as number 7 doesn't have atom ND1 that is required to build some atom (probably a hydrogen). So your residue and/or atom naming is not what GROMACS requires for your force field.
 
Mark
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