Hello!
I'm trying to simulate AKT1 protein in water, since this protein structure has a disulfide bond between two cysteine residues and some missing residues so I have to model the sequence with alphafold.
When I get the pdb file from alphafold the disulfide bond become disappear and I can't restore that bond.
I have used the -ss flag in pdb2gmx command and it didn't work!
So please guide me step by step to do this simulation with disulfide bond
Thanks.
Alireza Lashkaripour
Hello!
I'm not an expert in GROMACS, but I think since -ss flag in pdb2gmx did not work, you might need to manually specify disulfide bonds in the topology file. This can be done by editing the topology file (topol.top) and adding the disulfide bonds under [ bonds ] section.
Best regards,
-Ali
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