Re: [AMBER] Creating input file for Protein-protein simulation

From: David A Case <>
Date: Wed, 18 Apr 2012 07:56:42 -0400

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 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

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
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