[gmx-users] Help!

[Marc Ceruso]

It seems that you're PDB file contains hydrogens (NMR?). Try removing
hydrogens from your starting structure (whithin rasmol : select not
hydrogen and then write pdb newfile.pdb)
then run pdb2gmx -f newfile.pdb ....
M

On Fri, 26 Dec 2003, ankur gupta
wrote:

> Hi I am new in Gromacs and while trying to convert 1QHK.pdb file to
> gromacs file using pdb2gmx command encountered the following error.
>
> Fatal error: Atom HA1 is residue GLY 1 not found in rtp database while
> sorting atoms. May be different protonation state. Remove this hydrogen or
> choose a different protonation state. Option -ignh will ignore all
> hydrogen in the input.
>
> I have encountered similar type of error with other Proteins also. Please
> help me. Its really Urgent.
> Thanks
> Ankur Gupta
>
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