Sat Oct 8 11:37:52 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+sph.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 = amb.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 Sat Oct 8 2011 at 11:37:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 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: 0.5688991 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): -27.87300 34.70400 ymin,ymax (A): 38.12300 98.17600 zmin,zma (A): 30.38900 89.69900 x,y,z range (A): 62.57700 60.05300 59.31000 scale (grids/A): 0.5688991 object centre (A): 3.415499 68.14951 60.04400 number of atom coordinates read : 4461 total number of charged atoms : 4313 net assigned charge : -2.499956 assigned positive charge : 670.4571 centred at (gu) : 90.89538 88.31010 88.47704 assigned negative charge : -672.9602 centred at (gu) : 90.78518 88.40078 88.57039 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9064 nv = 96 ne = 84 npr = 95093 no. pairs analyzed = 95093 no. exposed pairs = 4775 no. arc points = 32618 no. surface atoms = 1635 nbur = 2826 mkacc time = 0.2400000 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 = 1.512000 m= 399 mr = 5391 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.5000000 number of dielectric boundary points 4040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3420 ## 398 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12082 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3868147E-09 -1.8158841E-09 midg,1,midg; midg,igrid,midg 2.3987057E-09 -1.7042484E-09 1,midg,midg; igrid,midg,midg -2.4246376E-09 2.5073454E-09 gauss-seidel spectral radius is 0.9841555 estimated iterations to convergence 65 setup time was (sec) 0.8200000 now iterating at: 11:37:53 rms-change max change #iterations 0.1111577 13.96117 at 10iterations 8.7074926E-03 1.049831 at 20iterations 8.5324823E-04 0.1073179 at 30iterations 1.8829906E-04 2.5924683E-02 at 40iterations 6.4603220E-05 9.2550814E-03 at 50iterations finished qdiffx linear iterations at : 11:37:58 total time elapsed so far: 5.260000 # loops : 50 mean,max change (kT/e) : 6.4603220E-05 9.2550814E-03 energy calculations done at 5.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.440000 DelPhi exited at 11:37:58 5.448u 0.464s 0:06.21 95.0% 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 Sat Oct 8 2011 at 11:37:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 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: 1.706697 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): -27.87300 34.70400 ymin,ymax (A): 38.12300 98.17600 zmin,zma (A): 30.38900 89.69900 x,y,z range (A): 62.57700 60.05300 59.31000 scale (grids/A): 1.706697 object centre (A): 3.415499 68.14951 60.04400 number of atom coordinates read : 4461 total number of charged atoms : 4313 net assigned charge : -2.499956 assigned positive charge : 670.4571 centred at (gu) : 92.68459 84.92948 85.42964 assigned negative charge : -672.9602 centred at (gu) : 92.35538 85.20182 85.71058 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 101282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32618 grid for indexing accessible points = 1.400000 m= 34724 mr = 74417 m= 4287 mr = 25933 m= 146 mr = 2575 m= 0 mr = 25 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5030 time to turn everything in is 0.8300000 number of dielectric boundary points 37489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 336 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 33373 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) : 0.5688991 object centre at (A) : 3.415499 68.14951 60.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9508283E-03 -2.4371875E-02 midg,1,midg; midg,igrid,midg 3.7497245E-02 3.5509698E-03 1,midg,midg; igrid,midg,midg -1.9772824E-02 3.3090167E-02 gauss-seidel spectral radius is 0.9984587 estimated iterations to convergence 202 setup time was (sec) 1.190000 now iterating at: 11:38:00 rms-change max change #iterations 4.619639 191.4366 at 10iterations 2.064193 62.40756 at 20iterations 0.9271860 29.49485 at 30iterations 0.4136393 12.90920 at 40iterations 0.1855218 4.762273 at 50iterations 8.2846120E-02 2.429361 at 60iterations 3.7220199E-02 1.044327 at 70iterations 1.6715387E-02 0.4859209 at 80iterations 7.5189103E-03 0.2067366 at 90iterations 3.4084860E-03 9.8247528E-02 at 100iterations 1.5627708E-03 4.1913986E-02 at 110iterations 7.3386909E-04 2.1778107E-02 at 120iterations finished qdiffx linear iterations at : 11:38:12 total time elapsed so far: 12.81000 # loops : 120 mean,max change (kT/e) : 7.3386909E-04 2.1778107E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 11:38:12 12.994u 0.535s 0:13.82 97.8% 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 Sat Oct 8 2011 at 11:38:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 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: 2.560046 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): -27.87300 34.70400 ymin,ymax (A): 38.12300 98.17600 zmin,zma (A): 30.38900 89.69900 x,y,z range (A): 62.57700 60.05300 59.31000 scale (grids/A): 2.560046 object centre (A): 3.415499 68.14951 60.04400 number of atom coordinates read : 4461 total number of charged atoms : 4313 net assigned charge : -2.499956 assigned positive charge : 670.4571 centred at (gu) : 94.02666 82.39404 83.14413 assigned negative charge : -672.9602 centred at (gu) : 93.53297 82.80257 83.56590 start vw surface at 0.1700000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 235936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32618 grid for indexing accessible points = 1.400000 m= 117736 mr = 180341 m= 37329 mr = 98166 m= 7300 mr = 30131 m= 665 mr = 5444 m= 15 mr = 378 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 16803 time to turn everything in is 2.150000 number of dielectric boundary points 84521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 34481 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) : 1.706697 object centre at (A) : 3.415499 68.14951 60.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5460745E-02 -0.2918794 midg,1,midg; midg,igrid,midg 0.5128059 -1.9122884E-02 1,midg,midg; igrid,midg,midg -0.2797711 0.2752241 gauss-seidel spectral radius is 0.9992355 estimated iterations to convergence 285 setup time was (sec) 2.560000 now iterating at: 11:38:15 rms-change max change #iterations 11.35522 292.5853 at 10iterations 6.564812 137.2307 at 20iterations 3.776708 69.41531 at 30iterations 2.170211 39.72189 at 40iterations 1.242214 21.21261 at 50iterations 0.7121686 12.56194 at 60iterations 0.4060277 7.525202 at 70iterations 0.2321999 3.574532 at 80iterations 0.1327287 2.253063 at 90iterations 7.5630322E-02 1.158469 at 100iterations 4.3227740E-02 0.7028656 at 110iterations 2.4659766E-02 0.4262466 at 120iterations 1.4055669E-02 0.2162800 at 130iterations 8.0333510E-03 0.1439457 at 140iterations 4.5888475E-03 7.1134567E-02 at 150iterations 2.6214351E-03 4.1929245E-02 at 160iterations 1.5073669E-03 2.3067474E-02 at 170iterations 8.6939277E-04 1.3935089E-02 at 180iterations finished qdiffx linear iterations at : 11:38:35 total time elapsed so far: 22.34000 # loops : 180 mean,max change (kT/e) : 8.6939277E-04 1.3935089E-02 energy calculations done at 22.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.50000 DelPhi exited at 11:38:36 22.509u 0.582s 0:23.43 98.5% 0+0k 0+0io 0pf+0w