After many times I have failed to run SAM 3.5 locally. So I think it's time for the author to say why it can't work with rosetta. But make_fragment.pl still has these rows in it:
# sam (secondary structure prediction software)
my $SAM_target99 = "...../target99"; # sam target99 executable
my $SAM_uniqueseq = ".....uniqueseq"; # sam uniqueseq executable
my $SAM_predict_2nd_dir = "...."; # sam predict-2nd directory
my $SAM_predict_2nd = "..."; # sam predict-2nd executable
Actually it doesn't work from 2.3 to 3.1, so long times!!!!!!!!!!!!!!!!
why does you guy not think of it during your development????????????????????
Can't put up with it!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
in app_membrane_abinitio.html: it says:
""""Fragment files Generate structural fragments only using SAM secondary structure prediction file (*.rdb) - jufo and psipred predict transmembrane helical regions poorly.""""
But it doesn't support it!!! Why!!!!!!!!!!!
I also found that the rdb file from SAM server web has an imcompatability format, and it can't used by rosetta directly.!!!!!!!!!!!!!!
So many problems!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!