* CHARMM Testcase pme_p21.inp * Author: Charles L. Brooks, III 20-Jan-98 * Files : top_all22_prot.inp, par_all22_prot.inp, * mbco_au_q0.crd, mono_p21.xtl, pme_p21.rst * Test : dynamics of restrained mbco in p21 crystal using pme after * deleting a high-pressure water. * !stream datadir.def bomlev -5 open unit 11 read card name top_all22_prot.inp read rtf unit 11 card close unit 11 read rtf card append * SO4 ion topology * 22 1 RESI SO4 -2.0 GROUP ATOM S S 0.0 ATOM O1 OC -0.5 ATOM O2 OC -0.5 ATOM O3 OC -0.5 ATOM O4 OC -0.5 BOND S O1 S O2 DOUBLE S O3 S O4 ACCEPTOR O1 S ACCEPTOR O2 S ACCEPTOR O3 S ACCEPTOR O4 S PATCHING FIRS NONE LAST NONE END open unit 11 read card name par_all22_prot.inp read param unit 11 card close unit 11 read param card append * SO4 Parameters * BOND OC S 400.0 1.43 ! from c25a1/toppar/param19.inp ANGLE OC S OC 85.0 109.5 ! FORCE CONSTANT JST A GUESS. END read sequence card * Myoglobin sequence * 153 VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HSD VAL TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HSD GLY GLN ASP ILE LEU ILE ARG LEU PHE LYS SER HSD PRO GLU THR LEU GLU LYS PHE ASP ARG PHE LYS HSD LEU LYS THR GLU ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HSD GLY VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS LYS LYS GLY HSP HSD GLU ALA GLU LEU LYS PRO LEU ALA GLN SER HSD ALA THR LYS HSE LYS ILE PRO ILE LYS TYR LEU GLU PHE ILE SER GLU ALA ILE ILE HSD VAL LEU HSD SER ARG HSP PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE ALA ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY generate MB read sequ HEME 1 generate HEM read sequ CO 1 generate CO read sequ TIP3 137 generate XTLW noangle nodihedral read sequ SO4 1 generate IONS read sequ TIP3 200 generate WAT noangle nodihedral open unit 11 read card name mbco_au_q0.crd read coor card unit 11 close unit 11 crystal define monoclinic 64.180 30.840 34.690 90.00 105.84 90.00 open unit 1 read card name mono_p21.xtl crystal read unit 1 card close unit 1 define prot sele segid mb .or. segid hem .or. segid co end coor stat sele segid wat end coor stat sele segid xtlw end coor stat sele prot end image byres sele .not. prot .and. .not. type h* end - xcen ?xave ycen ?yave zcen ?zave update inbf 0 cutim 4.0 coor stat sele segid wat end coor stat sele segid xtlw end !open read form unit 40 name @0pme_p21.rst open write form unit 41 name dyn.rst dyna verlet strt nstep 10 timestep 0.001 - iprfrq 1000 ihtfrq 0 ieqfrq 1000 - iuncrd -1 iunrea -1 iunwri 41 iunvel -1 kunit -1 - nprint 1 nsavc 0 nsavv 0 ihbfrq 0 - iasors 1 iasvel 1 iscvel 0 ichecw 0 - twindh 10.0 twindl -10.0 ntrfrq 1000 - inbfrq -1 atom vatom cutnb 12.0 ctofnb 10. cdie eps 1. - ctonnb 9.99 vshift cutim 14.0 imgfrq 25 wmin .5 - ewald pmewald kappa 0.32 order 6 fftx 80 ffty 36 fftz 48 - spline echeck 100000.0 firstt 300. finalt 300. tstruc 200. stop