Running MD for capped protein using Charm36 (charmm36_ljpme-jul2022.ff)

User discussions
1

GROMACS version: 2022.3
GROMACS modification: Yes/No

Hello,
I am trying to run MD for capped protein using Chamm36 forcefield (charmm36_ljpme-jul2022.ff). I need to select terminus residue from the following options:

Select start terminus type for ACE-0
0: NH3+
1: NH2
2: HYD1
3: MET1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None

Select end terminus type for NME-496
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None

Kindly advice which option to choose

2

Add the N-acetyl and N-methylamide protection to the N- and C-terminus, respectively, in a structure editor and select “None” for both

3

Hi slovas,

Thank you for your help. I tried that but following error pops up;

Program: gmx pdb2gmx, version 2022.3
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1096)

Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation