Tue Oct 11 08:31:59 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 Tue Oct 11 2011 at 08:31:59 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 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: 0.6727644 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): -17.83900 35.07700 ymin,ymax (A): -1.023000 50.64800 zmin,zma (A): -16.86000 31.21500 x,y,z range (A): 52.91600 51.67100 48.07500 scale (grids/A): 0.6727644 object centre (A): 8.618999 24.81250 7.177500 number of atom coordinates read : 2747 total number of charged atoms : 2616 net assigned charge : 3.500017 assigned positive charge : 420.3037 centred at (gu) : 89.16634 90.83471 89.56371 assigned negative charge : -416.8043 centred at (gu) : 89.06275 90.62277 89.43177 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8385 nv = 96 ne = 84 npr = 55432 no. pairs analyzed = 55432 no. exposed pairs = 3500 no. arc points = 24037 no. surface atoms = 1174 nbur = 1573 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 485 mr = 4686 m= 5 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2284 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9274437E-08 4.6219615E-08 midg,1,midg; midg,igrid,midg -4.2689052E-08 8.6968718E-08 1,midg,midg; igrid,midg,midg -2.1777367E-08 3.5812445E-08 gauss-seidel spectral radius is 0.9885598 estimated iterations to convergence 76 setup time was (sec) 0.4100000 now iterating at: 08:32:00 rms-change max change #iterations 0.1870703 30.81825 at 10iterations 2.1072837E-02 4.256603 at 20iterations 2.4029282E-03 0.3169575 at 30iterations 2.9731882E-04 3.5289764E-02 at 40iterations 4.6091463E-05 6.6146851E-03 at 50iterations finished qdiffx linear iterations at : 08:32:02 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.6091463E-05 6.6146851E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 08:32:03 3.456u 0.162s 0:03.98 90.7% 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 Tue Oct 11 2011 at 08:32:03 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 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: 2.018293 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): -17.83900 35.07700 ymin,ymax (A): -1.023000 50.64800 zmin,zma (A): -16.86000 31.21500 x,y,z range (A): 52.91600 51.67100 48.07500 scale (grids/A): 2.018293 object centre (A): 8.618999 24.81250 7.177500 number of atom coordinates read : 2747 total number of charged atoms : 2616 net assigned charge : 3.500017 assigned positive charge : 420.3037 centred at (gu) : 87.49853 92.50347 88.69058 assigned negative charge : -416.8043 centred at (gu) : 87.18802 91.86822 88.29501 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 89474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24037 grid for indexing accessible points = 1.400000 m= 33454 mr = 62385 m= 5829 mr = 24769 m= 408 mr = 3743 m= 8 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 814 time to turn everything in is 0.4400000 number of dielectric boundary points 38119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20729 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) : 0.6727644 object centre at (A) : 8.618999 24.81250 7.177500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7677561E-03 4.0050782E-02 midg,1,midg; midg,igrid,midg -4.1739453E-02 7.1840301E-02 1,midg,midg; igrid,midg,midg -1.7100228E-02 1.5157152E-02 gauss-seidel spectral radius is 0.9987954 estimated iterations to convergence 228 setup time was (sec) 0.6600000 now iterating at: 08:32:04 rms-change max change #iterations 4.931869 212.6376 at 10iterations 2.408957 68.67453 at 20iterations 1.181710 34.82064 at 30iterations 0.5799161 18.80386 at 40iterations 0.2859339 7.765368 at 50iterations 0.1400706 4.693365 at 60iterations 6.8742476E-02 2.036616 at 70iterations 3.3714663E-02 0.9164963 at 80iterations 1.6522370E-02 0.4964151 at 90iterations 8.1398450E-03 0.2370968 at 100iterations 4.0139691E-03 0.1167984 at 110iterations 1.9732751E-03 5.4309845E-02 at 120iterations finished qdiffx linear iterations at : 08:32:11 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.9732751E-03 5.4309845E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 08:32:12 7.998u 0.212s 0:08.58 95.5% 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 08:32:12 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 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: 3.027440 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): -17.83900 35.07700 ymin,ymax (A): -1.023000 50.64800 zmin,zma (A): -16.86000 31.21500 x,y,z range (A): 52.91600 51.67100 48.07500 scale (grids/A): 3.027440 object centre (A): 8.618999 24.81250 7.177500 number of atom coordinates read : 2747 total number of charged atoms : 2616 net assigned charge : 3.500017 assigned positive charge : 420.3037 centred at (gu) : 86.24760 93.75515 88.03584 assigned negative charge : -416.8043 centred at (gu) : 85.78193 92.80237 87.44240 start vw surface at 0.1000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 206087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24037 grid for indexing accessible points = 1.400000 m= 107012 mr = 150597 m= 40577 mr = 87683 m= 10805 mr = 32901 m= 1661 mr = 8181 m= 107 mr = 1101 m= 4 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 2526 time to turn everything in is 1.190000 number of dielectric boundary points 85739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 20928 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) : 2.018293 object centre at (A) : 8.618999 24.81250 7.177500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8113585E-02 0.1923137 midg,1,midg; midg,igrid,midg -0.3788289 0.9299603 1,midg,midg; igrid,midg,midg -0.1635441 7.5578466E-02 gauss-seidel spectral radius is 0.9993045 estimated iterations to convergence 299 setup time was (sec) 1.420000 now iterating at: 08:32:13 rms-change max change #iterations 11.29186 411.2042 at 10iterations 6.708753 129.1397 at 20iterations 3.966522 85.33768 at 30iterations 2.344425 43.77687 at 40iterations 1.384700 22.62243 at 50iterations 0.8154368 14.74167 at 60iterations 0.4806318 8.577241 at 70iterations 0.2825519 4.760838 at 80iterations 0.1658760 2.654167 at 90iterations 9.7170144E-02 1.546372 at 100iterations 5.7123262E-02 0.9287827 at 110iterations 3.3528004E-02 0.5680637 at 120iterations 1.9718587E-02 0.3146095 at 130iterations 1.1552815E-02 0.1978779 at 140iterations 6.8101529E-03 0.1139870 at 150iterations 4.0283524E-03 6.6584885E-02 at 160iterations 2.3986346E-03 4.3357849E-02 at 170iterations 1.4406820E-03 2.6595712E-02 at 180iterations finished qdiffx linear iterations at : 08:32:25 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 1.4406820E-03 2.6595712E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 08:32:25 12.861u 0.196s 0:13.45 97.0% 0+0k 0+0io 0pf+0w