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Difference between revisions of "protein.inp"
From MMTSB
(Input file for preparing the protein to do Replica exchange simulations) |
(No difference)
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Latest revision as of 14:57, 20 July 2009
!Read topologie open read card unit 10 name "$CHARMMDATA/top_all22_prot_cmap.inp" read rtf card unit 10 !Read parameters open read card unit 20 name "$CHARMMDATA/par_all22_prot_cmap.inp" read para card unit 20 read sequence card * sequence of phospholamban protein * 16 ! 1 2 3 4 5 6 7 8 9 10 GLY TRP TRP LEU ALA LEU ALA LEU ALA LEU ALA LEU ALA TRP TRP ALA generate PRO0 setup first ACE last CT3 ic param ic seed 1 N 1 CA 1 C ic build hbuild coor stat coor orie coor stat NBOND atom switch cdie vdw vswitch bycb - ctonnb 20.0 ctofnb 20.0 cutnb 24.0 mini sd nstep 100 nprint 10 step 0.005 inbfrq -1 imgfrq -1 mini abnr nstep 100 nprint 10 step 0.005 inbfrq -1 imgfrq -1 coor stat coor orie coor state coor rotate ydir 1.0 phi 90.0 coor state open write card unit 10 name pept.pdb write coor pdb unit 10 close unit 10 coor init coor stat select type CA end set ntot = ?nsel set i = 1 label ic_edit calc j = @i - 1 calc k = @i + 1 if j .ge. 1 then IC EDIT DIHE @j C @i N @i CA @i C -65.0 ! PHI END endif if k .le. @ntot then IC EDIT DIHE @i N @i CA @i C @k N -40.0 ! PSI END endif incr i by 1 if i .le. @ntot goto ic_edit ic param ic seed 1 N 1 CA 1 C ic build mini sd nstep 100 nprint 10 step 0.005 inbfrq -1 imgfrq -1 mini abnr nstep 100 nprint 10 step 0.005 inbfrq -1 imgfrq -1 open write card unit 10 name helix.pdb write coor pdb unit 10 close unit 10 stop