Mon Oct 10 14:14:25 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 Mon Oct 10 2011 at 14:14:25 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2500 !!! WARNING: ADP 667 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.6101323 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): 9.875000 68.22300 ymin,ymax (A): 5.223000 55.35200 zmin,zma (A): 77.55400 132.2120 x,y,z range (A): 58.34800 50.12900 54.65800 scale (grids/A): 0.6101323 object centre (A): 39.04900 30.28750 104.8830 number of atom coordinates read : 2500 total number of charged atoms : 2362 net assigned charge : -5.999993 assigned positive charge : 386.1578 centred at (gu) : 87.61558 90.08546 89.34924 assigned negative charge : -392.1585 centred at (gu) : 87.62350 90.01414 89.46435 start vw surface at 0.2500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 6365 nv = 96 ne = 84 npr = 48358 no. pairs analyzed = 48358 no. exposed pairs = 3574 no. arc points = 25118 no. surface atoms = 1184 nbur = 1316 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3158 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2473 ## 258 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 7739 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4476674E-09 -8.1323384E-09 midg,1,midg; midg,igrid,midg -7.0345028E-09 -5.2662472E-11 1,midg,midg; igrid,midg,midg -5.3590017E-09 -2.3870639E-09 gauss-seidel spectral radius is 0.9860946 estimated iterations to convergence 69 setup time was (sec) 0.7300000 now iterating at: 14:14:26 rms-change max change #iterations 0.1162315 18.61899 at 10iterations 1.0295202E-02 1.904964 at 20iterations 8.8334823E-04 0.1422768 at 30iterations 8.0159618E-05 1.2195587E-02 at 40iterations 7.0629694E-06 1.2893677E-03 at 50iterations finished qdiffx linear iterations at : 14:14:30 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 7.0629694E-06 1.2893677E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 14:14:30 4.334u 0.198s 0:04.87 92.8% 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 Mon Oct 10 2011 at 14:14:30 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2500 !!! WARNING: ADP 667 has a net charge of -2.0000 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: 1.830397 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): 9.875000 68.22300 ymin,ymax (A): 5.223000 55.35200 zmin,zma (A): 77.55400 132.2120 x,y,z range (A): 58.34800 50.12900 54.65800 scale (grids/A): 1.830397 object centre (A): 39.04900 30.28750 104.8830 number of atom coordinates read : 2500 total number of charged atoms : 2362 net assigned charge : -5.999993 assigned positive charge : 386.1578 centred at (gu) : 82.84627 90.25584 88.04703 assigned negative charge : -392.1585 centred at (gu) : 82.87025 90.04225 88.39271 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 68655 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25118 grid for indexing accessible points = 1.400000 m= 23271 mr = 45322 m= 3358 mr = 15868 m= 184 mr = 1826 m= 0 mr = 48 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 32404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 18502 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) : 0.6101323 object centre at (A) : 39.04900 30.28750 104.8830 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7484624E-03 -2.8951865E-02 midg,1,midg; midg,igrid,midg -1.5969733E-02 -9.2533892E-03 1,midg,midg; igrid,midg,midg 7.4616298E-03 2.3334187E-02 gauss-seidel spectral radius is 0.9985327 estimated iterations to convergence 207 setup time was (sec) 1.050000 now iterating at: 14:14:32 rms-change max change #iterations 3.989537 167.4914 at 10iterations 1.799013 67.14491 at 20iterations 0.8193580 30.29663 at 30iterations 0.3720785 12.33333 at 40iterations 0.1691257 6.395123 at 50iterations 7.6830842E-02 2.831662 at 60iterations 3.4983832E-02 1.125419 at 70iterations 1.5866719E-02 0.5067325 at 80iterations 7.2414516E-03 0.2341919 at 90iterations 3.2920102E-03 0.1111660 at 100iterations 1.4989302E-03 5.3836823E-02 at 110iterations 6.8162044E-04 2.1648407E-02 at 120iterations finished qdiffx linear iterations at : 14:14:41 total time elapsed so far: 10.04000 # loops : 120 mean,max change (kT/e) : 6.8162044E-04 2.1648407E-02 energy calculations done at 10.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.27000 DelPhi exited at 14:14:42 10.273u 0.239s 0:11.32 92.7% 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 Mon Oct 10 2011 at 14:14:42 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2500 !!! WARNING: ADP 667 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.745595 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): 9.875000 68.22300 ymin,ymax (A): 5.223000 55.35200 zmin,zma (A): 77.55400 132.2120 x,y,z range (A): 58.34800 50.12900 54.65800 scale (grids/A): 2.745595 object centre (A): 39.04900 30.28750 104.8830 number of atom coordinates read : 2500 total number of charged atoms : 2362 net assigned charge : -5.999993 assigned positive charge : 386.1578 centred at (gu) : 79.26924 90.38350 87.07041 assigned negative charge : -392.1585 centred at (gu) : 79.30536 90.06326 87.58894 start vw surface at 0.2000000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 158908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25118 grid for indexing accessible points = 1.400000 m= 76333 mr = 110983 m= 25820 mr = 59585 m= 5870 mr = 19549 m= 743 mr = 4010 m= 26 mr = 436 m= 0 mr = 8 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.700000 number of dielectric boundary points 73129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 18894 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) : 1.830397 object centre at (A) : 39.04900 30.28750 104.8830 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1293049E-02 -0.2865904 midg,1,midg; midg,igrid,midg -0.1258780 -0.1292371 1,midg,midg; igrid,midg,midg 3.2459792E-02 0.6858369 gauss-seidel spectral radius is 0.9992388 estimated iterations to convergence 286 setup time was (sec) 2.070000 now iterating at: 14:14:44 rms-change max change #iterations 9.718980 333.7644 at 10iterations 5.718803 134.1907 at 20iterations 3.330801 79.28334 at 30iterations 1.930727 47.81094 at 40iterations 1.112271 24.94729 at 50iterations 0.6372486 13.30903 at 60iterations 0.3660156 7.687315 at 70iterations 0.2091815 4.543465 at 80iterations 0.1196384 2.582131 at 90iterations 6.8655238E-02 1.394176 at 100iterations 3.9086953E-02 0.7555389 at 110iterations 2.2353480E-02 0.4732323 at 120iterations 1.2726313E-02 0.2369432 at 130iterations 7.2621172E-03 0.1475391 at 140iterations 4.1423026E-03 8.4874153E-02 at 150iterations 2.3612916E-03 4.3767929E-02 at 160iterations 1.3447871E-03 2.7580261E-02 at 170iterations 7.6764758E-04 1.5305042E-02 at 180iterations finished qdiffx linear iterations at : 14:14:56 total time elapsed so far: 14.18000 # loops : 180 mean,max change (kT/e) : 7.6764758E-04 1.5305042E-02 energy calculations done at 14.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.41000 DelPhi exited at 14:14:57 14.411u 0.269s 0:15.07 97.3% 0+0k 0+0io 0pf+0w