Dear all,

I am trying to model a protein with a ligand using the "/." construct in the alignment and I am getting the following error:

[ralf@localhost models]$ mod8v2 tens1.top forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read Image PC Routine Line Source mod8v2_i386-intel 0837011A Unknown Unknown Unknown mod8v2_i386-intel 0836E555 Unknown Unknown Unknown mod8v2_i386-intel 0834064D Unknown Unknown Unknown ... mod8v2_i386-intel 080811C6 Unknown Unknown Unknown mod8v2_i386-intel 08080D81 Unknown Unknown Unknown libc.so.6 006F179A Unknown Unknown Unknown mod8v2_i386-intel 08080CC1 Unknown Unknown Unknown [ralf@localhost models]$

[ralf@localhost models]$ tail -20 tens1.log read_al_374_> Non-standard residue type,position,sequence: . 324 1 read_al_374_> Non-standard residue type,position,sequence: . 324 2

Read the alignment from file : tens1.ali Total number of alignment positions: 324

# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1d5r 308 2 1d5r . 2 tensin1 309 2 tensin1 . TOP_________> 129 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'EQ'

TOP_________> 130 117 CHECK_ALIGNMENT

check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL 1d5r.pdb

Dynamically allocated memory at amaxstructure [B,kB,MB]: 2652691 2590.519 2.530 openf5__224_> Open 11 OLD SEQUENTIAL 1d5r.pdb [ralf@localhost models]$

I should mention that the modelling process without ligand runs smoothly. I am using Modeller 8v2 on Linux RHE, 2.4.21-47.0.1.ELsmp kernel.

Thanks in advance for any hints,

Ralf