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