[gmx-users] protein topology

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Oct 27 08:53:07 CET 2015

Hi Nikhil,

The hydrogens are added by pdb2gmx. The -ignh flag is just to ignore
(additional) hydrogens in the input.


On Oct 27, 2015 08:32, "Nikhil Maroli" <scinikhil at gmail.com> wrote:

> Dear all,
> I wanted to do Protein ligand MD i followed as per the tutorial,when i use
> pdb2gmx -f ach.pdb and selecting GROMOS96 43a1 force field
>  and SPC water it shows an error
> Atom HB1 in residue ASP 5 was not found in rtp entry ASP with 11 atoms
> while sorting atoms.
> when i checked rtp and input files there is only 9 atoms in rtp so i
> couldnt understand what i change i have to make in input files
> so i put -ignh flag
> it works fine but i need hydrogen atoms
> can anyone tell me how to fix it ?
> thanks
> Nikhil
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