AMBER Archive (2009)

Subject: [AMBER] Problem with "Atom does not have a type"

From: Richard Tseng (richard617_at_gmail.com)
Date: Thu Mar 26 2009 - 18:17:19 CDT

Hi all,

I am trying to study interaction between a protein and a RNA sequence.
During the preparation for topology and coordinate files, I have one
simple problem when I used Amber 10 (Interestingly, there is no
problem in Amber 8).

I first tried to generate topology and coordinate files for the RNA sequence.
After loading the corresponding pdb file into leap, there are message indicates
a fatal error, atom does not have a type.
I have searched through the forum for solution (I think about using
nucgen and nab.
However, both methods does not satisfy my needs. I also tried to use
addAtomType.
It did not work.). None can solve this simple problem.
The reason that works in Amber 8 is that I use antechamber (loadmol2)
to define atom type
and bond type for each nucleotide. Before load pdb files in leap, I
load mol2 file first. In this way,
there are no such error messages. However, after I do the same procedure in
Amber 10, it shows the error message "Fatal Error: last line
read:........" rather than
"atom does not have a type".

Could anyone share some thoughts on this and maybe solutions? Thanks a lot!! 

-- 
Chih-Yuan Tseng (Richard)
Postdoctoral fellow,
Department of Oncology
University of Alberta
Cross Cancer Institute
Edmonton, AB T6G 1Z2 Canada
Office: Sun life building 14Fl
Office phone no.: 1-780-6434440
Cell: 1-780-9082104
Email: chih-yuan.tseng_at_ualberta.ca; richard617_at_gmail.com
Homepage: http://richardcyt.myweb.hinet.net/
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