On Wed, Apr 18, 2012, Tommy Yap wrote:
>
> The problem is that some of the residue coordinates in their respective pdb
> file collide with some residues from the other protein's pdb file. When i
> combine using text editor and view the pdb file using VMD, the structure
> looks very weird...is there any way other that this?
Molecular dynamics simulations require a starting structure, and in fact,
require a "good" starting structure (generally speaking). If you wish to "run
MD between the proteins", you need to figure out what initial relative
configuration you want, and then create a pdb file that has that
configuration.
If you want the two proteins to be interacting with each other, you probably
need to some protein-protein docking software to create such initial
configurations. If you want something else, then some other tool may be
useful; e.g. you could just use VMD to pull the two proteins apart so that
they don't overlap.
...good luck...dac
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Received on Wed Apr 18 2012 - 05:00:05 PDT
