I have looked at the manual and previous queries posted on this
reoccuring subject but am unable to get modeller to model a protein-DNA
complex where I treat the DNA as a rigid body.
All I get back are models of the protein with no DNA present.
1. Use Modeller 9v1, which has much improved support for ligands.
2. Use a Python script to build your model - TOP has been deprecated for
a long time.
3. See http://salilab.org/modeller/9v1/manual/node18.html for an input
file to build a model with HETATM residues preserved as rigid bodies.
There is no need to modify your PDB file, unless it is obviously
non-standard in some way. As long as your DNA is in HETATM records,
Modeller should pick it up just fine.
2. Included in my alignment file a '.' for each BLK residue and a '/' to
signifiy the end of a chain
>P1;1AAA
sequence:1AAA:FIRST :@ END : : :human:undefined: 0.00: 0.00
RTAYTNTQLLELEKEFHFNKYLCRPRRVEIAALLDLTERKVKVWFQNRRMKHKRQTQ*
Your models don't contain the DNA, because you're not listing it in the
target sequence here. The DNA ligands and/or chain breaks also need to
be in your target sequence. See the URL above for an example alignment.