On 18/04/12, aiswarya pawar <aiswarya.pa...@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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