Sat Oct 8 11:36:06 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 Sat Oct 8 2011 at 11:36:06 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4561 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5707598 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): -27.33100 35.04200 ymin,ymax (A): 34.89600 95.02000 zmin,zma (A): 30.43100 90.55900 x,y,z range (A): 62.37300 60.12400 60.12800 scale (grids/A): 0.5707598 object centre (A): 3.855499 64.95800 60.49500 number of atom coordinates read : 4561 total number of charged atoms : 4400 net assigned charge : -5.499943 assigned positive charge : 688.4225 centred at (gu) : 90.87971 89.07739 88.78082 assigned negative charge : -693.9262 centred at (gu) : 90.71460 89.18418 88.95158 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9451 nv = 96 ne = 84 npr = 96591 no. pairs analyzed = 96591 no. exposed pairs = 5043 no. arc points = 34744 no. surface atoms = 1711 nbur = 2850 mkacc time = 0.2800000 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 = 1.484000 m= 413 mr = 5511 m= 0 mr = 37 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.5500000 number of dielectric boundary points 4316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3571 ## 399 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 12455 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3493431E-09 -4.0096473E-09 midg,1,midg; midg,igrid,midg 2.0963191E-09 -2.9710345E-09 1,midg,midg; igrid,midg,midg -4.2263721E-09 3.8295673E-09 gauss-seidel spectral radius is 0.9842705 estimated iterations to convergence 66 setup time was (sec) 0.8200000 now iterating at: 11:36:07 rms-change max change #iterations 0.1159623 16.80180 at 10iterations 8.8932980E-03 1.302406 at 20iterations 8.8567997E-04 0.1050186 at 30iterations 1.7508019E-04 2.3692608E-02 at 40iterations 5.6157536E-05 7.9190731E-03 at 50iterations finished qdiffx linear iterations at : 11:36:11 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 5.6157536E-05 7.9190731E-03 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 11:36:11 4.423u 0.302s 0:05.12 92.1% 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 Sat Oct 8 2011 at 11:36:11 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4561 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.712279 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): -27.33100 35.04200 ymin,ymax (A): 34.89600 95.02000 zmin,zma (A): 30.43100 90.55900 x,y,z range (A): 62.37300 60.12400 60.12800 scale (grids/A): 1.712279 object centre (A): 3.855499 64.95800 60.49500 number of atom coordinates read : 4561 total number of charged atoms : 4400 net assigned charge : -5.499943 assigned positive charge : 688.4225 centred at (gu) : 92.63766 87.23061 86.34139 assigned negative charge : -693.9262 centred at (gu) : 92.14308 87.55173 86.85429 start vw surface at 0.2100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 105247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34744 grid for indexing accessible points = 1.400000 m= 35291 mr = 76497 m= 4521 mr = 26156 m= 151 mr = 2684 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 7731 time to turn everything in is 0.9000000 number of dielectric boundary points 39839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 34074 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) : 0.5707598 object centre at (A) : 3.855499 64.95800 60.49500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1405725E-02 -3.1030675E-02 midg,1,midg; midg,igrid,midg 1.9444002E-02 -1.7944764E-02 1,midg,midg; igrid,midg,midg -2.7679753E-02 3.5933297E-02 gauss-seidel spectral radius is 0.9984872 estimated iterations to convergence 204 setup time was (sec) 1.210000 now iterating at: 11:36:13 rms-change max change #iterations 4.759269 179.4738 at 10iterations 2.137189 66.18313 at 20iterations 0.9650857 27.00358 at 30iterations 0.4344611 14.42294 at 40iterations 0.1952604 5.118059 at 50iterations 8.8570684E-02 2.385218 at 60iterations 3.9889678E-02 1.085371 at 70iterations 1.8045155E-02 0.5253906 at 80iterations 8.1398413E-03 0.2257814 at 90iterations 3.6971699E-03 0.1068649 at 100iterations 1.6882084E-03 4.7613144E-02 at 110iterations 7.7926030E-04 2.1998048E-02 at 120iterations finished qdiffx linear iterations at : 11:36:22 total time elapsed so far: 10.07000 # loops : 120 mean,max change (kT/e) : 7.7926030E-04 2.1998048E-02 energy calculations done at 10.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.26000 DelPhi exited at 11:36:22 10.261u 0.334s 0:10.96 96.6% 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 Sat Oct 8 2011 at 11:36:22 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4561 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.568419 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): -27.33100 35.04200 ymin,ymax (A): 34.89600 95.02000 zmin,zma (A): 30.43100 90.55900 x,y,z range (A): 62.37300 60.12400 60.12800 scale (grids/A): 2.568419 object centre (A): 3.855499 64.95800 60.49500 number of atom coordinates read : 4561 total number of charged atoms : 4400 net assigned charge : -5.499943 assigned positive charge : 688.4225 centred at (gu) : 93.95623 85.84529 84.51167 assigned negative charge : -693.9262 centred at (gu) : 93.21440 86.32755 85.28136 start vw surface at 0.2200000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 244550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34744 grid for indexing accessible points = 1.400000 m= 119878 mr = 185413 m= 37731 mr = 99201 m= 7719 mr = 30122 m= 835 mr = 5863 m= 14 mr = 494 m= 0 mr = 2 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 25606 time to turn everything in is 2.300000 number of dielectric boundary points 89632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 2.470000 number of grid points assigned charge 35169 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) : 1.712279 object centre at (A) : 3.855499 64.95800 60.49500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2989259 -0.3703000 midg,1,midg; midg,igrid,midg 0.2955250 -0.3059233 1,midg,midg; igrid,midg,midg -0.1989223 0.3359696 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 2.660000 now iterating at: 11:36:25 rms-change max change #iterations 11.62512 341.8642 at 10iterations 6.767756 138.0314 at 20iterations 3.923723 68.88083 at 30iterations 2.268551 42.42763 at 40iterations 1.306540 22.27144 at 50iterations 0.7542751 13.39498 at 60iterations 0.4330069 6.881554 at 70iterations 0.2485877 3.861275 at 80iterations 0.1425839 2.335338 at 90iterations 8.1640258E-02 1.271011 at 100iterations 4.6848595E-02 0.7771077 at 110iterations 2.6851753E-02 0.4560032 at 120iterations 1.5394668E-02 0.2391453 at 130iterations 8.8239508E-03 0.1354713 at 140iterations 5.0699101E-03 7.9598427E-02 at 150iterations 2.9173780E-03 4.6317101E-02 at 160iterations 1.6870270E-03 2.7400970E-02 at 170iterations 9.8225172E-04 1.6796112E-02 at 180iterations finished qdiffx linear iterations at : 11:36:40 total time elapsed so far: 17.72000 # loops : 180 mean,max change (kT/e) : 9.8225172E-04 1.6796112E-02 energy calculations done at 17.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.91000 DelPhi exited at 11:36:41 17.907u 0.332s 0:18.56 98.2% 0+0k 0+0io 0pf+0w