unanswered Backmapping multiple chain systems leads to broken molecules

  • amin_sagar
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1 year 1 month ago #9618 by amin_sagar
Dear Martini Users/Developers,
I simulated a two chain protein system with Martini using gromacs. I then extracted the frames from the trajectory and made sure that all the frames have the protein intact (no pbc artefacts).
I then tried to backmap the frames to All atom structures as I need to calculate the SAXS profiles. But, backmapping using Backward ( github.com/Tsjerk/Backward ). However, the output All-atom structure is broken, I think, do to PBC effects.
The initial structure generated by backward.py is fine but the energy minimized and equilibrated structures are all broken. I can repair some of the structures with pbc wrapping using trjconv but this doesn't work on all the structures.
Has anyone else experiences this error before?
Is the procedure for backmapping multi-chain proteins different.
The command I use is
./Backward-v5/initram-v5.sh -f Frame_9.gro -p topol.top -to charmm36
I would be really grateful for any suggestions.

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