[AMBER] Leap. Error messages on renaming ASP to AS4 etc.

From: George Tzotzos <gtzotzos.me.com>
Date: Thu, 14 Jun 2012 17:52:13 +0200

I am trying to generate a topology file for a low pH MD simulation.

I renamed the HIS, GLU and ASP residues in the starting PDB file to HIP, GL4, AS4.

For tleap I'm using leaprc.ff99SB

Loading my protein.pdb file I get, for example,

Unknown residue: AS4 number: 5 type: Nonterminal
etc.

Trying to save the topology file, generates FATAL errors of the type

FATAL: Atom .R<AS4 7>.A<N 1> does not have a type.

I checked the mail archive and couldn't find anything that could help me solve this problem.

Your help will be appreciated

Best regards

George
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Received on Thu Jun 14 2012 - 09:00:02 PDT
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