Fatal error:

Atom HB3 in residue ASP 144 was not found in rtp entry NASP with 14 atoms

while sorting atoms.

For a hydrogen, this can be a different protonation state, or it

might have had a different number in the PDB file and was rebuilt

(it might for instance have been H3, and we only expected H1 & H2).

Note that hydrogens might have been added to the entry for the N-terminus.

Remove this hydrogen or choose a different protonation state to solve it.

Option -ignh will ignore all hydrogens in the input.

while i use ignh, it would affect the simulation

Did you try to use the pdb2pqr server and then convert the output to PDB (using Openbabel)?

thanks @Luciano.. it worked.. but sooner i get one more error while running ions.mdp file and it fails to generate .tpr pile as

gmx grompp -f ions.mdp -c 123_solv.gro -p topol.top -o ions.tpr

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

Setting the LD random seed to 938284221

WARNING 1 [file topol.top, line 23]:

Too few gb parameters for type SOL

Couldn't find topology match for atomtype SOL

Aborted (core dumped)

I suggest following the tutorial below:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html

Regards,