You will learn that some forcefields are nicer than others to get parameters for unknown/weird molecules, although sometimes you don't have much of a choice of which one to use. Then, as you get more comfortable, dive into these details. You can use VMD for that, or otherwise Pymol. In 'VMD movie Generator' diagonal-box, it initially shows Stage: 0 of 0, and Progress 0 of 0.
My suggestion is to mutate that KCX lysine to a regular lysine and the other D-aminoacid to an L-aminoacid. I am trying to gnerate a movie of my amber-8 trajectory file(a.prmtop and a.mdcrd). When you have something that falls outside this dataset, you're in trouble. Problem is, they only have a dataset for the most common ones: mostly canonical amino acids and nucleic acids.
Vmd movie maker software#
Software like VMD try to match a combination of residue naming and bonding information to an internal database to find the right parameters for your molecules. Assigning these parameters to a molecule from its coordinates is called parameterization. This topology is the collection of all physico-chemical parameters that describe your molecule(s), such as bond lengths, bond angles, dihedrals, atomic charges, etc. psf, you are creating the topology of your system. One is a D-aminoacid, another is a phosphate moiety, and the last one is a modified lysine.
If you look at the RCSB PDB page for your protein ( here), you see that there are a couple of entries in the small molecules section (scroll down on the page).
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