We have placed a dimer protein into gromacs energy minimization utilising OPLS force fields. but after running 9567 its get minimized. But the problem is that after energy minimization one gap which is present inside the input structure got connected with out adding the amino acids that should not be needed for me.
What should I do?
General "issue" in modelling packages with renumbering of the protein sequences and therefor connecting the sequential AA. In my research I use a conversion script to adjust the MD output numbering to the input crystal.
If it's a small gap (loop-like) and the full sequence is known, you can simply reconstitute the loop, using various modelling tools.
No actually I want keep the chain as a gap. Our input molecule also had that gap. so what will be solution?
I can only tell for the AMBER package but I am pretty sure it is the same with GROMACS (little experience). Try to rename the individual "domains" before and after the gap with a different sequence ID in pdb and add a terminate statement in between. Not sure if the numbering will be kept, but the gap definitely should be kept.
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