Membrane protein structure prediction setup.

python ~/openmmawsem/mm_create_project.py 5HT1A.fasta get something like

7065232773324643260 MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPEDRSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCRQ 00000000000000000000000000000000000001111111111111111111111111100000001111111111111111111111111100000000000001111111111111111111111000000000000000000000011111111111111110000000000000000000000000000111111111111111111111111000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111110000000000001111111111111111111111100000000000000000000

from http://pureseqtm.predmp.com/

convert it to "PredictedZim". Jpred(http://www.compbio.dundee.ac.uk/jpred/) to get ssweight. and mm_run_with_pulling_start.py