I've been working on a homology model of a spanning helical membrane protein. The options I'm using seem to work for a somewhat similar protein, so I can't figure out what the problem is. Essentially, the problem with the decoys is two fold:
1. The helices do not bundle, nor do they consistently stay approximately normal to the membrane. I get very spread out structures with most helices lying 'flat' in the membrane.
2. The scoring seems to reward these bad structures. Even if I randomly get some better looking decoys, the flat and spread out structures consistently score better.
I've also noticed something odd. One of these loops sometimes fails to close- when that happens, the energy skyrockets, but the decoys do not spread out. In fact, they don't move much at all. So when the loops close successfully I get too much movement, but when they fail I get no movement.
Any help would be greatly appreciated. I have a lot of speculations on the cause of this problem, but none of the changes I've tried has had an appreciable impact. I'll just paste my options here, it would be a lot easier to give all my inputs if I could upload a zipped directory. I've included my threaded structure and some sample outputs.
Oh, and I know the construct count is low. But since bad structures are scoring well anyway, I've been experimenting with changing inputs with small numbers of constructs.
-loops:loop_file commons.loops ##loop file
-loops:extended true #force phi-psi angles to be set to 180 degrees independent of loop input file (recommended for production runs)
-loops:idealize_after_loop_close #give idealized phi and psi angles after loop has been closed
-loops:relax fastrelax #does a minimization of the structure in the torsion space
-loops:fast #decreases the monte carlo inner and outer cycles of loop rebuilding, greatly decreasing computation time
-out:file:fullatom #output file will be full-atom
-ex1 #Include extra chi1 rotamers
-nstruct 10 #number of models to build. 1000 recommended for production runs
-loops:frag_sizes 9 3 1
-loops:frag_files aat000_09_05.200_v1_3 aat000_03_05.200_v1_3 none #these fragmentfiles are concatenated from chain A repeats (3x) and chain E
#membrane specific terms
#-membrane_center -0.0236 72.00924 168.745
#-membrane_normal 0.0 0.0 -1.0