[gmx-users] Gromax don't recognize -ignh command

[Mark Abraham]

Hi,

I expect that's a hydrogen in an NH3+ group being added as a terminus to
your protein.  You might want to tell pdb2gmx to stop trying to help with
the termini, with -ter or -noter.

Mark

On Sun, 29 Dec 2019 at 13:02, ali khamoushi <khamuoshia at gmail.com> wrote:

> Hello everyone
> I have PDB file which have directly downloaded from RCSB.org
> but when I want to do the procedure of simulation, I get this error:
> Fatal error:
> Atom HA3 in residue GLY 1 was not found in rtp entry GLY with 9 atoms
> while sorting atoms.
>
> I have searched and find that the solution is to run the -ignh command. but
> gromacs does'nt recognize it.
> my code for first step is:
> ‫‪gmx‬‬ ‫‪pdb2gmx‬‬ ‫‪-f‬‬ ‫‪protein-nolig.pdb‬‬ ‫‪-water‬‬ ‫‪tip3p‬‬
> ‫‪-ignh‬‬ ‫‪-o‬‬ ‫‪conf.gro‬‬
> or this:
>
> gmx pdb2gmx -f protein.pdb -o protein.gro‬‬ -water tip3p -ignh
>
> but neither is working.
> my forcefield is charmm36 and changing the forcefield didn't help.
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