Re: [AMBER] How to prepare the same prmtop from two PDBs for NED analysis?

From: case <>
Date: Wed, 28 Jul 2010 08:08:32 -0400

On Wed, Jul 28, 2010, Catein Catherine wrote:
> I could like to do a NED calculation. I start with two protein
> structure I downloaded from PDB (before and after activation). I
> understand I need to get the same prmtop file from these PDB files.
> As the results were given by two groups, although the number of residues
> and resides's name are the same (I have make them to be the same
> manually). I found the prmtop generated from these two PDB files are
> still different. It is because the order/name of atoms appears in the
> PDB files are different.

The order of atoms within a residue in the input PDB file should be
irrelevant, and not show up in the resulting prmtop file. Since we don't know
what the differences are between the two prmtop files, nor how you prepared
the prmtop files, we can't help much more.


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Received on Wed Jul 28 2010 - 05:30:05 PDT
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