Pdb2gmx command stops/hangs

User discussions
1

GROMACS version: 2021.1
GROMACS modification: No

Hi, I am very a much new user. Seemed to have installed gromacs ("$ gmx pdb2gmx –version" gives the correct version). I have installed it on a Ubuntu 20.4 PC. I am trying the first tutorial at NMR Spectroscopy Research Group

When I run the following command, it stops/hangs:
$ gmx pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh
It hangs at this step: “15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)”

Any assistance will be much appreciated?
Best wishes
Gert Kruger

2

Hi,
gmx pdb2gmx lists all the force fields implemented in GROMACS, did you try to select one by typing the corresponding number?
Best regards
Alessandra

3

Thanks! I did not read properly! Yes, I was supposed to choose “GROMOS 53a6 force field and the SPC water model”. That works.
Many thanks!