Hi all, I have a problem with VMD wrap and alignment. I simulated a docked RNA and protein complex, but when I wrap the complex following link (https://www.researchgate.net/post/how_to_use_pbc_wrap_command_in_vmd_to_re-center_a_multimeric_protein) for the most part it works with some frames having the complex as monomers at either end of the box. However, when I align the complex to try and center everything the protein goes to one end of the box while the nucleic is held in the middle.
Has anyone had this issue and found a remedy? Thanks!
Hi Yasir, I have but it doesn’t seem to work. I should’ve updated this and said it was resolved!
for those of you having the same issue, i did wrapped based on the link I posted, I changed the residue to fragment and aligned based on a single nucleotide at the interface of the subunits
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