Error while sorting atoms

User discussions
1

GROMACS version:2021
GROMACS modification: No
Hi!
I am working on palmitoilation of protein. I have attached palm group in CYS195 using CHARMM-GUI. When I try to run pdb2gmx, I am getting error.
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790)

Fatal error:
Atom C1 in residue CYS 1 was not found in rtp entry CYSH with 10 atoms
while sorting atoms.
.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Please help me out!!!
Thanks in advance.

2

why do you want to run `

gmx pdb2gmx

` when you can make the protein from charmm-gui? prepare the full simulation system and run those files.

3

Thank you sir! I’ll try doing that