Tue Oct 11 06:24:37 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 Tue Oct 11 2011 at 06:24:37 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1316 !!! WARNING: SEP 97 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.8045016 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): -14.81400 25.53000 ymin,ymax (A): 42.62400 76.67400 zmin,zma (A): -4.691000 39.56000 x,y,z range (A): 40.34400 34.05000 44.25100 scale (grids/A): 0.8045016 object centre (A): 5.358001 59.64899 17.43450 number of atom coordinates read : 1316 total number of charged atoms : 1266 net assigned charge : 2.025002 assigned positive charge : 202.5574 centred at (gu) : 90.01814 89.98043 89.80394 assigned negative charge : -200.5323 centred at (gu) : 90.14613 90.01315 89.51660 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6377 nv = 96 ne = 84 npr = 24440 no. pairs analyzed = 24440 no. exposed pairs = 1736 no. arc points = 12357 no. surface atoms = 603 nbur = 713 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 580 mr = 3640 m= 7 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 862 ## 72 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6022 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1586034E-07 7.0574748E-07 midg,1,midg; midg,igrid,midg 2.0249345E-07 6.1852504E-08 1,midg,midg; igrid,midg,midg 4.0119519E-07 -1.4494026E-07 gauss-seidel spectral radius is 0.9918618 estimated iterations to convergence 90 setup time was (sec) 0.4200000 now iterating at: 06:24:37 rms-change max change #iterations 0.2707036 40.60869 at 10iterations 4.1661713E-02 5.299148 at 20iterations 6.7345011E-03 0.9272575 at 30iterations 1.0880134E-03 0.1514854 at 40iterations 2.1084503E-04 2.9891253E-02 at 50iterations finished qdiffx linear iterations at : 06:24:40 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 2.1084503E-04 2.9891253E-02 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 06:24:40 3.043u 0.166s 0:03.67 87.1% 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 Tue Oct 11 2011 at 06:24:40 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1316 !!! WARNING: SEP 97 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.413505 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): -14.81400 25.53000 ymin,ymax (A): 42.62400 76.67400 zmin,zma (A): -4.691000 39.56000 x,y,z range (A): 40.34400 34.05000 44.25100 scale (grids/A): 2.413505 object centre (A): 5.358001 59.64899 17.43450 number of atom coordinates read : 1316 total number of charged atoms : 1266 net assigned charge : 2.025002 assigned positive charge : 202.5574 centred at (gu) : 90.05473 89.94154 89.41196 assigned negative charge : -200.5323 centred at (gu) : 90.43859 90.03967 88.54996 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65979 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12357 grid for indexing accessible points = 1.400000 m= 29270 mr = 45887 m= 7616 mr = 22778 m= 977 mr = 5503 m= 61 mr = 548 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 29161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 10106 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) : 0.8045016 object centre at (A) : 5.358001 59.64899 17.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1382742E-02 7.0738986E-02 midg,1,midg; midg,igrid,midg 1.0371945E-02 4.5528128E-03 1,midg,midg; igrid,midg,midg 7.6878168E-02 1.1781340E-02 gauss-seidel spectral radius is 0.9989966 estimated iterations to convergence 250 setup time was (sec) 0.8000000 now iterating at: 06:24:41 rms-change max change #iterations 4.571286 224.5261 at 10iterations 2.392756 86.16266 at 20iterations 1.250758 42.30205 at 30iterations 0.6511133 19.60652 at 40iterations 0.3397635 10.57774 at 50iterations 0.1779821 5.368613 at 60iterations 9.2713252E-02 2.660764 at 70iterations 4.8608717E-02 1.490109 at 80iterations 2.5340620E-02 0.7683868 at 90iterations 1.3302631E-02 0.4019489 at 100iterations 7.0138611E-03 0.2102313 at 110iterations 3.7251983E-03 0.1188154 at 120iterations finished qdiffx linear iterations at : 06:24:47 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 3.7251983E-03 0.1188154 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 06:24:48 6.990u 0.207s 0:07.56 95.1% 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 Tue Oct 11 2011 at 06:24:48 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1316 !!! WARNING: SEP 97 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.620257 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): -14.81400 25.53000 ymin,ymax (A): 42.62400 76.67400 zmin,zma (A): -4.691000 39.56000 x,y,z range (A): 40.34400 34.05000 44.25100 scale (grids/A): 3.620257 object centre (A): 5.358001 59.64899 17.43450 number of atom coordinates read : 1316 total number of charged atoms : 1266 net assigned charge : 2.025002 assigned positive charge : 202.5574 centred at (gu) : 90.08221 89.91237 89.11803 assigned negative charge : -200.5323 centred at (gu) : 90.65801 90.05947 87.82504 start vw surface at 0.1200000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 151334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12357 grid for indexing accessible points = 1.400000 m= 86358 mr = 109976 m= 41452 mr = 72478 m= 15166 mr = 35024 m= 3834 mr = 12309 m= 627 mr = 2906 m= 82 mr = 427 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.610000 number of dielectric boundary points 65677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 10128 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) : 2.413505 object centre at (A) : 5.358001 59.64899 17.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6472623 0.4536810 midg,1,midg; midg,igrid,midg 4.4100761E-02 3.8265780E-02 1,midg,midg; igrid,midg,midg 0.5792909 4.2931428E-03 gauss-seidel spectral radius is 0.9993290 estimated iterations to convergence 305 setup time was (sec) 1.890000 now iterating at: 06:24:50 rms-change max change #iterations 9.731042 288.3000 at 10iterations 5.874332 134.9740 at 20iterations 3.526567 73.51881 at 30iterations 2.116032 47.37058 at 40iterations 1.259496 27.29780 at 50iterations 0.7512107 14.48629 at 60iterations 0.4469461 9.905750 at 70iterations 0.2653675 5.364777 at 80iterations 0.1579190 2.975191 at 90iterations 9.3772434E-02 1.634743 at 100iterations 5.5636063E-02 1.027161 at 110iterations 3.3011951E-02 0.7578239 at 120iterations 1.9578908E-02 0.3787689 at 130iterations 1.1643236E-02 0.2226868 at 140iterations 6.9330232E-03 0.1253052 at 150iterations 4.1798828E-03 8.2344055E-02 at 160iterations 2.5597657E-03 5.3452969E-02 at 170iterations 1.6253573E-03 3.4397125E-02 at 180iterations finished qdiffx linear iterations at : 06:25:00 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 1.6253573E-03 3.4397125E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.53000 DelPhi exited at 06:25:00 11.534u 0.211s 0:12.17 96.4% 0+0k 0+0io 0pf+0w