Hello,
I am trying to do MMGBSA analysis for a protein-peptide system. I extracted the complex.prmtop, receptor.prmtop and peptide.prmtop topology files from the step5_input.parm7 file.
I run the mmgbsa analysis using this command line but I am getting this error-
MMPBSA.py -O -i mmpbsa.in -o output.dat -sp step5_input.parm7 -cp com.prmtop -rp rec.prmtop -lp peptide.prmtop -y md-combined-all.nc
PrmtopError: Topology files have no Implicit radii! You can add implicit radii using xparmed.py or parmed.py
Fatal Error!
Is there a way to add the implicit radii to the topology files? I also wanted to inform that I have prepared my system using charmm-gui with charmm36m forcefields and not amber forcefield.
With Regards
Keya Joshi
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Received on Mon Mar 04 2024 - 08:00:02 PST
