After running MD simulations in Desmond (Schrödinger) I wanted to analyse the trajectory files of two monomeric structures of the same enzyme (one mutant and one WT) but when I used Multiseq in VMD for RMSD calculations, I saw that ligands' and metal ion's sequences were changed. They should have appear at the end of the sequences but they were implemented into the sequences after 260th residue (i.e. 259,260,601,602,603,261,262,263...) for both.
When I use STAMP for structural alignment and try to plot RMSD vs Residue graph it can not calculate the RMSD values after the 260th residue and the plot shows a flat trend at zero starting from the 260th residue.
These ligands and residues are far away from each other that I cannot find a reason why Multiseq would change the sequence or Desmond would build a sequence like this during system building or simulation.
Most tools in VMD are very sensitive to the order in which residues are actually written into the PDB file. I wonder if that's what's going on here? One thing to note: unlike most other VMD tools, Multiseq uses chain names rather than segnames to identify individual components. An easy workaround for you would be to simply give all your ions and ligands some other chain name before running Multiseq.
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