Hello Andy and Darren, thanks for the help. You were right about the composition of the pdb file containing an acetylated group. This change to the .ali file allowed the models to be generated.
>P1;4mdhA structureX:4mdhA: 1 :A: 333 :A:undefined:undefined:-1.00:-1.00 SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEE IAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKE NFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFIT TVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISD-GNSYGVPDDLLYSFPVTIK-DKTWK IVEGLPINDFSREKMDLTAKELAEEKETAFEFLSSA-* >P1;TvLDH sequence:TvLDH: : : : ::: 0.00: 0.00 MSEAAHVLITGAAGQIGYILSHWIASGELYG-DRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPK AAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPE NFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHD-YVFDTFFK KIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIH VVEGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG*
I appreciate your help.
Andrew Latos MBB student University of Idaho