Hi Sindrila,
You are best off posting such messages to the AMBER mailing list which I
have cc'd here. Go to
http://lists.ambermd.org/ for details on how to signup
and post messages to the list.
What you are seeing is that your pdb file contains residues that are not in
the standard amino acid / dna templates. Likely it contains some kind of
cofactor such as NADH, HEME etc. You should look closely at it to see what
it is and then read the literature on other simulations of such systems. You
should also take a look at the tutorials on the AMBER Website.
http://ambermd.org/tutorials/ in particular pay attention to tutorial B4:
http://ambermd.org/tutorials/basic/tutorial4b/index.htm
All the best
Ross
From: Sindrila Dutta banik [mailto:sindrila.duttabanik.yahoo.com]
Sent: Saturday, May 07, 2011 6:08 AM
To: ross.rosswalker.co.uk
Subject: Problem related to the Amber
Dear Sir,
I am a new user of Amber. I am facing a problem as I am going to load a pdb
file in xleap or tleap. It gives some error message like
'the file contains 192 atoms not in the residue template'
Will you please tell me how to get the 'residue template' and how to modify
the pdb file.
With best regards
Sindrila Dutta Banik
University of Kalyani
Kalyani, West Bengal
India
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Received on Sun May 08 2011 - 22:00:02 PDT
