Hi,

Please check the format of the alignment file (there was another recent similar question). If this does not help, please email us the input top, alignment, and PDB files.

Thanks, ANdrej

-- Andrej Sali, Associate Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali@rockefeller.edu; http://salilab.org

-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Karen C. Ellis Sent: Monday, January 21, 2002 11:30 AM To: modeller_usage@salilab.org Subject: malign3D question

I was trying to use the malign3D command to do an alignment of three sequences based on their PDB structures. I was able to get an inital alignment from the command malign with no problems. I used this alignment as the starting point. I then copied the commands found on the user manual page for malign3d (of course changing the file names as appropriate) to a .top file. When I look at the .log file I get the following error

fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0

I have also tried running align3d for two sequences at a time and that works fine. Any suggestions on what I am doing wrong?

Thanks, Karen Ellis