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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?

Karen Ellis