GROMACS version: 2018
GROMACS modification: Yes/No
My protein crystal structure contains only oxygen atoms of the water molecules. So using Chimera hydrogen were added to the system and then the output was used to pdb2gmx conversion. Force field I am using is Charmm36. The protonation and non protonation type for the residues were selected as follows.
Lysine, Arginine - protonated
Glutamine, Aspartic acid, Glutamic acid - not protonated
Histidine: H on NE2 only (HSE)
For the N terminal MET82 I selected NH3+ and C terminal LEU was COO-.
But this gave an error: Atom HB3 in residue MET82 was not found in rtp entry MET with 19 atoms while sorting atoms
The command I used was gmx pdb2gmx -f pro00.pdb -inter -p system.top -o pro01.pdb
Can some one please tell me what is the mistake and how to solve this?
The problem was solved. The atom type of the hydrogen added through chimera are different in rtp file. So changed atom type according to rtp.
But does any one know how the hydrogen atoms of the SPCE water model are named in Charmm36 force field. The atom type of the water hydrogen?
Just for posterity, your problem was not with atom types but with atom names. These are two different concepts, since atom type is a force field parameter concept related to LJ terms.
For SPC/E, look in the spce.itp file:
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OWSPCE 1 SOL OW 1 -0.8476
2 HWSPCE 1 SOL HW1 1 0.4238
3 HWSPCE 1 SOL HW2 1 0.4238
Although we provide this topology if users want to try it, I would strongly urge you to use the validated water model for use with CHARMM36, which is the CHARMM-modified TIP3P (the default in tip3p.itp that we distribute with the CHARMM force field). Use of SPC/E is essentially untested and you run the risk of invalid simulations.