I am doing point mutations in PYMOL and I want to run molecular dynamics (MD) to see the effect of the mutation in the stability of my protein. In order to use the software Amber that does the MD I have to have the file in PDB, but once I do the mutation in PYMOL I cannot save it as PDB it only saves it as session. Do you know how can I do that? Or can someone tell me another alternative to my approach?
It can save in PDB format
It can save in PDB format
Just to add to it: you can also use SCWRL (http://dunbrack.fccc.edu/scwrl4/) which is the standard in performing in silico mutations. The advantage here is the fact that it will calculate a large number of possible conformers of the new residue, and select the best one.
i did the same thing by typing out the command but the structure appeared to be different from the original file (.pse)
is there any settings to play around to ensure this not happen?
The .pse file is the proprietary PyMOL workspace file, it contains not only all the object you imported into PyMOL, but also their current representation, orientation is space and so on. It allows you to resume your PyMOL session at exactly the point where you saved it. Most other programs cannot understand the .pse file.
In contrast, the .pdb file is a plain text file basically listing the atoms and residues of your molecule with their coordinates. It is an old standard format for macromolecular coordinates that all molecule viewers understand and can work with.
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