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

ali khamoushi khamuoshia at gmail.com
Sun Dec 29 14:02:33 CET 2019


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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