Simulation with nucleotide

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
Hi,
I am Aradhya. I have face problem while running gmx pdb2gmx command and i had getting following errors.
Fatal error: (1 protein)
Residue 17 named ARG of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
Fatal error:(2 protein)
Residue ‘’ not found in residue topology database

2

This means you have a missing or incorrectly named atom. In the case of the former, you will have to reconstruct it using modeling software of your preference. In the case of the latter, simply correct the name in the input file.

This error suggests incorrect syntax in your input coordinate file.

3

Thank you Jalemkul

4

The error was resolved, but i am again getting the following error.

Fatal error:
1 particles communicated to PME rank 2 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
How can i fix it ?

5

https://manual.gromacs.org/current/user-guide/run-time-errors.html#x-particles-communicated-to-pme-node-y-are-more-than-a-cell-length-out-of-the-domain-decomposition-cell-of-their-charge-group