Dear Professor Case and Professor Maingi
Thank you for your advices.
I used "savePdb" of LEaP module to make pdb file.
This is because I defined such an unusual residue
by either PREPIN or MOL2 file format.
Using "desc" command,
I found that connection0/1 was not properly set,
Exactly, when I used PREP file.
Such a connection was not set at all
When I used MOL2 files.
I appreciate your supports, again.
Yours sincerely,
Ikuo KURISAKI
PS
The following web page would be helpful
If one want to set connect0/1/2.
It shows an example for the command.
e.g. "set RC5.1 connect1 RC5.1.O3'"
http://archive.ambermd.org/201202/0013.html
-----Original Message-----
From: kurisaki [mailto:kurisaki.ncube.human.nagoya-u.ac.jp]
Sent: Tuesday, March 05, 2013 6:38 PM
To: 'AMBER Mailing List'
Subject: [AMBER] Annomalous "TER" is inserted in a peptide including
non-standard AA
Dear Amber developers and users,
When I build an poly-peptide including non-standard amino acid (AA),
Annomalous "TER" is sometime inserted between standard and
Non-standard one in PDB formatted file.
Here, I prepared the prepin file for the non-standard AA
By using ANTECHAMBER and make polypeptide by "sequence" command of LEaP.
After loading the residue-related files, i.e. PREPIN and MOL2 files,
I set head and tail for these residues.
Why does such an anomalous TER appear?
In other word, how do I make LEaP recognize a RESIDUE is isolated,
Where thus Ter must be inserted.
I am really glad if you give advices.
Yours sincerely,
Ikuo KURISAKI
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Received on Tue Mar 05 2013 - 05:30:04 PST
