Sun Oct 9 10:39:00 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 10:39:00 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 !!! WARNING: HIR 211 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5403355 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 39.40800 104.3670 ymin,ymax (A): 3.341000 69.22600 zmin,zma (A): -13.16200 39.78000 x,y,z range (A): 64.95900 65.88499 52.94200 scale (grids/A): 0.5403355 object centre (A): 71.88750 36.28350 13.30900 number of atom coordinates read : 3221 total number of charged atoms : 3072 net assigned charge : -4.985970 assigned positive charge : 475.3813 centred at (gu) : 90.74503 90.91073 89.71337 assigned negative charge : -480.3692 centred at (gu) : 90.58875 90.89077 89.58488 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6323 nv = 96 ne = 84 npr = 62046 no. pairs analyzed = 62046 no. exposed pairs = 4818 no. arc points = 34486 no. surface atoms = 1588 nbur = 1633 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 283 mr = 2832 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3374 ## 423 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0860071E-09 4.4526269E-10 midg,1,midg; midg,igrid,midg -2.9532832E-10 -1.7053853E-10 1,midg,midg; igrid,midg,midg -9.7667707E-10 7.7054546E-10 gauss-seidel spectral radius is 0.9823830 estimated iterations to convergence 62 setup time was (sec) 0.6200000 now iterating at: 10:39:01 rms-change max change #iterations 7.0208423E-02 10.79749 at 10iterations 4.5703519E-03 0.8945808 at 20iterations 3.0957756E-04 5.7121277E-02 at 30iterations 2.3836112E-05 4.9524307E-03 at 40iterations 2.7750721E-06 5.3691864E-04 at 50iterations finished qdiffx linear iterations at : 10:39:04 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.7750721E-06 5.3691864E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 10:39:04 3.619u 0.180s 0:04.09 92.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 10:39:04 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 !!! WARNING: HIR 211 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.621006 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 39.40800 104.3670 ymin,ymax (A): 3.341000 69.22600 zmin,zma (A): -13.16200 39.78000 x,y,z range (A): 64.95900 65.88499 52.94200 scale (grids/A): 1.621006 object centre (A): 71.88750 36.28350 13.30900 number of atom coordinates read : 3221 total number of charged atoms : 3072 net assigned charge : -4.985970 assigned positive charge : 475.3813 centred at (gu) : 92.23396 92.73068 89.13911 assigned negative charge : -480.3692 centred at (gu) : 91.76591 92.67216 88.75418 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 70169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34486 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19756 mr = 44119 m= 1891 mr = 11914 m= 52 mr = 721 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 0.5600000 number of dielectric boundary points 35114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 23520 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5403355 object centre at (A) : 71.88750 36.28350 13.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1301724E-03 1.1656349E-02 midg,1,midg; midg,igrid,midg -1.7061500E-02 -1.4873449E-02 1,midg,midg; igrid,midg,midg -2.4147645E-02 1.5239258E-02 gauss-seidel spectral radius is 0.9982090 estimated iterations to convergence 188 setup time was (sec) 0.8800000 now iterating at: 10:39:06 rms-change max change #iterations 3.407804 168.6339 at 10iterations 1.420176 54.65607 at 20iterations 0.5918733 24.90870 at 30iterations 0.2463045 9.028930 at 40iterations 0.1031697 3.595138 at 50iterations 4.3084353E-02 1.509819 at 60iterations 1.8045245E-02 0.6940145 at 70iterations 7.5602182E-03 0.2853146 at 80iterations 3.1509998E-03 0.1382613 at 90iterations 1.3224555E-03 4.7889709E-02 at 100iterations 5.5649027E-04 1.9556046E-02 at 110iterations 2.3253239E-04 8.6603165E-03 at 120iterations finished qdiffx linear iterations at : 10:39:13 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 2.3253239E-04 8.6603165E-03 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.870000 DelPhi exited at 10:39:14 8.869u 0.202s 0:09.41 96.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 10:39:14 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 !!! WARNING: HIR 211 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.431510 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 39.40800 104.3670 ymin,ymax (A): 3.341000 69.22600 zmin,zma (A): -13.16200 39.78000 x,y,z range (A): 64.95900 65.88499 52.94200 scale (grids/A): 2.431510 object centre (A): 71.88750 36.28350 13.30900 number of atom coordinates read : 3221 total number of charged atoms : 3072 net assigned charge : -4.985970 assigned positive charge : 475.3813 centred at (gu) : 93.35069 94.09570 88.70823 assigned negative charge : -480.3692 centred at (gu) : 92.64871 94.00814 88.13119 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 163391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34486 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 68684 mr = 109665 m= 18149 mr = 50559 m= 2698 mr = 12190 m= 151 mr = 1424 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 267 time to turn everything in is 1.280000 number of dielectric boundary points 79183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 24550 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.621006 object centre at (A) : 71.88750 36.28350 13.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1303515 0.1795164 midg,1,midg; midg,igrid,midg -0.4196507 -0.2745133 1,midg,midg; igrid,midg,midg -0.2711059 0.3413124 gauss-seidel spectral radius is 0.9991568 estimated iterations to convergence 272 setup time was (sec) 1.600000 now iterating at: 10:39:16 rms-change max change #iterations 9.058574 330.3367 at 10iterations 5.166371 158.5551 at 20iterations 2.924968 69.91495 at 30iterations 1.648954 36.26200 at 40iterations 0.9253678 20.12564 at 50iterations 0.5157068 11.27635 at 60iterations 0.2872903 5.953564 at 70iterations 0.1595175 3.667271 at 80iterations 8.8457644E-02 1.915123 at 90iterations 4.9007624E-02 0.9760532 at 100iterations 2.7188519E-02 0.5461636 at 110iterations 1.5038306E-02 0.3095179 at 120iterations 8.3180508E-03 0.1719475 at 130iterations 4.6025952E-03 9.3410015E-02 at 140iterations 2.5434331E-03 5.2456856E-02 at 150iterations 1.4040020E-03 2.8676987E-02 at 160iterations 7.7965693E-04 1.6263962E-02 at 170iterations 4.3036466E-04 9.4451904E-03 at 180iterations finished qdiffx linear iterations at : 10:39:27 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 4.3036466E-04 9.4451904E-03 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 10:39:28 13.087u 0.240s 0:13.65 97.5% 0+0k 0+0io 0pf+0w