Re: [AMBER] how to convert to standard Amber PDB input

From: case <>
Date: Tue, 30 Mar 2010 08:24:14 -0400

On Tue, Mar 30, 2010, geyan wrote:

> I construct a PDB file of a DNA-Protein complex,with three molecular
> protein and one molecular DNA. But the Atom numbers and residue numbers
> are not consecutive,which is seperated by the mark "MODEL".But from
> many Amber examples,I found that these two items are consecutive. SO
> how can I convert this irregular format to the standard one?Will this
> affect the Amber computaion?

The PDB card MODEL usually separates alternate conformations for the *same*
molecule(s). TER cards are used to separate molecules. It's not clear how
you constructed your pdb file.

Amber doesn't care much about the input atom numbers or residue numbers,
so you are probably fine. Don't be afraid to experiment! Loading your
PDB file into LEaP will give you an answer far faster and better than
sending email to the list.


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Received on Tue Mar 30 2010 - 05:30:02 PDT
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