Sat Oct 15 15:13:06 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 15 2011 at 15:13:07 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3132 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6009250 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): -31.28200 26.16500 ymin,ymax (A): 17.94200 77.18400 zmin,zma (A): -20.45800 34.67500 x,y,z range (A): 57.44700 59.24200 55.13300 scale (grids/A): 0.6009250 object centre (A): -2.558499 47.56300 7.108500 number of atom coordinates read : 3132 total number of charged atoms : 2976 net assigned charge : -1.499988 assigned positive charge : 474.0570 centred at (gu) : 89.51642 88.56604 90.51266 assigned negative charge : -475.5582 centred at (gu) : 89.55685 88.79063 90.58521 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 62003 no. pairs analyzed = 62003 no. exposed pairs = 4447 no. arc points = 30222 no. surface atoms = 1484 nbur = 1648 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3641 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3038 ## 306 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9332 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2192834E-09 -4.6845066E-09 midg,1,midg; midg,igrid,midg 1.2929785E-08 -8.2082980E-09 1,midg,midg; igrid,midg,midg 1.1734135E-09 -2.3913740E-09 gauss-seidel spectral radius is 0.9857185 estimated iterations to convergence 69 setup time was (sec) 0.7100000 now iterating at: 15:13:08 rms-change max change #iterations 0.1187466 17.62203 at 10iterations 1.0046462E-02 1.661108 at 20iterations 8.5842231E-04 0.1352768 at 30iterations 8.0922939E-05 1.2226105E-02 at 40iterations 1.2987102E-05 2.5792122E-03 at 50iterations finished qdiffx linear iterations at : 15:13:11 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 1.2987102E-05 2.5792122E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 15:13:12 4.315u 0.256s 0:05.09 89.5% 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 Sat Oct 15 2011 at 15:13:12 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3132 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.802775 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): -31.28200 26.16500 ymin,ymax (A): 17.94200 77.18400 zmin,zma (A): -20.45800 34.67500 x,y,z range (A): 57.44700 59.24200 55.13300 scale (grids/A): 1.802775 object centre (A): -2.558499 47.56300 7.108500 number of atom coordinates read : 3132 total number of charged atoms : 2976 net assigned charge : -1.499988 assigned positive charge : 474.0570 centred at (gu) : 88.54879 85.69750 91.53722 assigned negative charge : -475.5582 centred at (gu) : 88.67025 86.37157 91.75493 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 79599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30222 grid for indexing accessible points = 1.400000 m= 26794 mr = 51693 m= 3678 mr = 18365 m= 163 mr = 1931 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 38215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 247 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 23209 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) : 0.6009250 object centre at (A) : -2.558499 47.56300 7.108500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3990206E-02 -3.6454978E-03 midg,1,midg; midg,igrid,midg 3.2049093E-02 -4.1109417E-02 1,midg,midg; igrid,midg,midg 8.1871999E-03 -2.1622442E-02 gauss-seidel spectral radius is 0.9985408 estimated iterations to convergence 208 setup time was (sec) 1.060000 now iterating at: 15:13:13 rms-change max change #iterations 4.234372 201.2841 at 10iterations 1.922907 70.41518 at 20iterations 0.8697438 29.11726 at 30iterations 0.3971955 12.18587 at 40iterations 0.1800935 5.989258 at 50iterations 8.2078271E-02 2.664660 at 60iterations 3.7486687E-02 1.114065 at 70iterations 1.7042970E-02 0.5475690 at 80iterations 7.7577722E-03 0.2517776 at 90iterations 3.5515395E-03 0.1116419 at 100iterations 1.6190007E-03 4.8736572E-02 at 110iterations 7.4203126E-04 2.4650574E-02 at 120iterations finished qdiffx linear iterations at : 15:13:22 total time elapsed so far: 9.860000 # loops : 120 mean,max change (kT/e) : 7.4203126E-04 2.4650574E-02 energy calculations done at 9.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.05000 DelPhi exited at 15:13:22 10.055u 0.320s 0:10.74 96.5% 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 Sat Oct 15 2011 at 15:13:23 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3132 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.704163 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): -31.28200 26.16500 ymin,ymax (A): 17.94200 77.18400 zmin,zma (A): -20.45800 34.67500 x,y,z range (A): 57.44700 59.24200 55.13300 scale (grids/A): 2.704163 object centre (A): -2.558499 47.56300 7.108500 number of atom coordinates read : 3132 total number of charged atoms : 2976 net assigned charge : -1.499988 assigned positive charge : 474.0570 centred at (gu) : 87.82300 83.54593 92.30570 assigned negative charge : -475.5582 centred at (gu) : 88.00543 84.55733 92.63233 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 184039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30222 grid for indexing accessible points = 1.400000 m= 87739 mr = 126861 m= 29708 mr = 68287 m= 6128 mr = 22467 m= 722 mr = 4138 m= 31 mr = 416 m= 0 mr = 6 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.860000 number of dielectric boundary points 86192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 23804 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) : 1.802775 object centre at (A) : -2.558499 47.56300 7.108500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1415416 1.7233841E-02 midg,1,midg; midg,igrid,midg 0.3588149 -0.5864288 1,midg,midg; igrid,midg,midg 0.1629956 -0.2716210 gauss-seidel spectral radius is 0.9992544 estimated iterations to convergence 289 setup time was (sec) 2.200000 now iterating at: 15:13:25 rms-change max change #iterations 10.43283 345.3349 at 10iterations 6.168974 145.3721 at 20iterations 3.604742 84.01380 at 30iterations 2.101277 45.76307 at 40iterations 1.221482 24.25687 at 50iterations 0.7062230 13.94383 at 60iterations 0.4090542 7.659042 at 70iterations 0.2355290 4.598255 at 80iterations 0.1359021 2.537879 at 90iterations 7.8166440E-02 1.436661 at 100iterations 4.4896066E-02 0.8574677 at 110iterations 2.5885236E-02 0.4540815 at 120iterations 1.4837367E-02 0.2788467 at 130iterations 8.5254824E-03 0.1543331 at 140iterations 4.9096472E-03 9.1348648E-02 at 150iterations 2.8265633E-03 5.1506042E-02 at 160iterations 1.6368718E-03 3.1614304E-02 at 170iterations 9.5364067E-04 2.0504832E-02 at 180iterations finished qdiffx linear iterations at : 15:13:40 total time elapsed so far: 17.11000 # loops : 180 mean,max change (kT/e) : 9.5364067E-04 2.0504832E-02 energy calculations done at 17.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.30000 DelPhi exited at 15:13:41 17.301u 0.352s 0:17.98 98.1% 0+0k 0+0io 0pf+0w