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

From: Catein Catherine <askamber23.hotmail.com>
Date: Wed, 28 Jul 2010 12:27:55 +0800

Dear Sir/Madam,


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.


It could be a huge amount of work or induce more error if I correct it manually. I am writing to ask if there are any smart way to synergize these two PDB files so that I make the input files easily?


Best regards,


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Received on Tue Jul 27 2010 - 21:30:07 PDT
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