Segmentation Fault (Energy Minimization)

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
I am trying to simulate a alpha fold predicted structure. I am using gromosFFG54A8 forcefield. but am an error " segmentation fault (core dumped)" .
I didn’t get this error when I used the same forcefield for PDB structures nor did i get the error when I use GROMOS96 53a6 to simulate the same alphafold structure. I am just confused as what could be the reason and is there a way I can use gromos 54A8 to simulate this protein. i am keep on using this particular forcefield because it contains parameters for some post translational modifications

2

Hi Maham,

A few suggestions.

  1. When you open your GRO file (after converting the PDB to GRO) in a visualizer (like VMD), do you get any rendering warnings? Sometimes when PTMs are added by webservers, they are placed in odd configurations and cause clashes (at least I’ve had that happen a few times). If you see odd renderings/clashes, you can try to apply small displacements to remove the clashes and then re-run grompp and try energy minimizing again.

  2. If not obvious clashes are present, one other thing to consider is trying to run the minimization using a double precision build of gromacs for a few steps. If there is a clash that is hard to find visually, running in double precision will let you know if there is a very large energy (corresponding to a likely clash/unreal overlap) and then you can deal with it accordingly.

Hope that helps.

-Mick

3

Thank you for the suggestions.
There are no apparent warnings shown. I tired to perform EM on the Alphafold structure using the 54A8 but still got the same error. but I was able to energy minimized the structure using gromacs provides parameters.
Can any one test this forcefield with some alpha fold predicted structure? (Downloads | Vienna-PTM 2.0)