On 12/29/19 2:54 PM, Mark Abraham wrote:
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.
HA3 isn't a terminal proton in the CHARMM force field so I doubt that's
it. The full screen output from pdb2gmx would be informative here.
-Justin
Mark
On Sun, 29 Dec 2019 at 13:02, ali khamoushi <khamuos...@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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