Wed Dec 21 14:21:14 PST 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 Wed Dec 21 2011 at 14:21:14 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6402302 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): -3.970000 34.72300 ymin,ymax (A): -3.623000 47.92300 zmin,zma (A): -24.43500 31.17000 x,y,z range (A): 38.69300 51.54600 55.60500 scale (grids/A): 0.6402302 object centre (A): 15.37650 22.15000 3.367500 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 285.1041 centred at (gu) : 90.37168 92.70781 90.06512 assigned negative charge : -284.0643 centred at (gu) : 90.45205 92.88348 90.03344 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5495 nv = 96 ne = 84 npr = 40243 no. pairs analyzed = 40243 no. exposed pairs = 2455 no. arc points = 17233 no. surface atoms = 835 nbur = 1118 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 281 mr = 3108 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2700000 number of dielectric boundary points 2637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1712 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8273875E-10 4.7641642E-09 midg,1,midg; midg,igrid,midg 9.3587316E-09 -2.4233392E-08 1,midg,midg; igrid,midg,midg 8.1133997E-09 -5.3085008E-09 gauss-seidel spectral radius is 0.9873034 estimated iterations to convergence 73 setup time was (sec) 0.7500000 now iterating at: 14:21:16 rms-change max change #iterations 0.1231755 23.19240 at 10iterations 1.2158304E-02 1.955601 at 20iterations 1.2159152E-03 0.2064955 at 30iterations 1.1724267E-04 2.0380020E-02 at 40iterations 1.1689556E-05 2.0122528E-03 at 50iterations finished qdiffx linear iterations at : 14:21:23 total time elapsed so far: 7.640000 # loops : 50 mean,max change (kT/e) : 1.1689556E-05 2.0122528E-03 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 14:21:28 7.866u 0.690s 0:14.55 58.7% 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 Wed Dec 21 2011 at 14:21:30 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.920691 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): -3.970000 34.72300 ymin,ymax (A): -3.623000 47.92300 zmin,zma (A): -24.43500 31.17000 x,y,z range (A): 38.69300 51.54600 55.60500 scale (grids/A): 1.920691 object centre (A): 15.37650 22.15000 3.367500 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 285.1041 centred at (gu) : 91.11520 98.12357 90.19547 assigned negative charge : -284.0643 centred at (gu) : 91.35644 98.65071 90.10046 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 59010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 22096 mr = 40972 m= 3411 mr = 16911 m= 179 mr = 2284 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2076 time to turn everything in is 0.6200000 number of dielectric boundary points 24472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 14383 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) : 0.6402302 object centre at (A) : 15.37650 22.15000 3.367500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2224538E-02 7.3121851E-03 midg,1,midg; midg,igrid,midg 3.1448696E-02 -1.7834224E-02 1,midg,midg; igrid,midg,midg 4.6344865E-03 -5.4332917E-03 gauss-seidel spectral radius is 0.9985781 estimated iterations to convergence 210 setup time was (sec) 1.170000 now iterating at: 14:21:33 rms-change max change #iterations 3.595841 151.4798 at 10iterations 1.657123 57.71919 at 20iterations 0.7650551 27.22419 at 30iterations 0.3551294 13.12503 at 40iterations 0.1625137 5.827115 at 50iterations 7.5011186E-02 2.756313 at 60iterations 3.4518164E-02 1.235058 at 70iterations 1.5975118E-02 0.5877094 at 80iterations 7.3369103E-03 0.2708931 at 90iterations 3.3935499E-03 0.1405735 at 100iterations 1.5662165E-03 5.7561874E-02 at 110iterations 7.2153792E-04 2.4822235E-02 at 120iterations finished qdiffx linear iterations at : 14:21:49 total time elapsed so far: 17.39000 # loops : 120 mean,max change (kT/e) : 7.2153792E-04 2.4822235E-02 energy calculations done at 17.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.57000 DelPhi exited at 14:21:59 17.578u 0.721s 0:28.82 63.4% 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 Wed Dec 21 2011 at 14:22:00 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.881036 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): -3.970000 34.72300 ymin,ymax (A): -3.623000 47.92300 zmin,zma (A): -24.43500 31.17000 x,y,z range (A): 38.69300 51.54600 55.60500 scale (grids/A): 2.881036 object centre (A): 15.37650 22.15000 3.367500 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 285.1041 centred at (gu) : 91.67274 102.1855 90.29321 assigned negative charge : -284.0643 centred at (gu) : 92.03458 102.9761 90.15073 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 136220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 70567 mr = 98838 m= 26452 mr = 58797 m= 6138 mr = 22092 m= 745 mr = 4836 m= 40 mr = 495 m= 0 mr = 15 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 6839 time to turn everything in is 1.340000 number of dielectric boundary points 55089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 14568 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) : 1.920691 object centre at (A) : 15.37650 22.15000 3.367500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.039973 -2.8593156E-02 midg,1,midg; midg,igrid,midg 0.3256454 -0.2088537 1,midg,midg; igrid,midg,midg 2.1924991E-02 -3.2838799E-02 gauss-seidel spectral radius is 0.9992281 estimated iterations to convergence 284 setup time was (sec) 1.930000 now iterating at: 14:22:03 rms-change max change #iterations 8.488280 423.9951 at 10iterations 4.858881 120.6871 at 20iterations 2.759845 59.06056 at 30iterations 1.566592 34.88721 at 40iterations 0.8897694 18.18588 at 50iterations 0.5033873 10.47552 at 60iterations 0.2862102 6.363835 at 70iterations 0.1618709 3.541060 at 80iterations 9.1637239E-02 2.076299 at 90iterations 5.1907197E-02 1.028472 at 100iterations 2.9500015E-02 0.6029043 at 110iterations 1.6666440E-02 0.3273020 at 120iterations 9.4471090E-03 0.1796217 at 130iterations 5.3580180E-03 0.1132500 at 140iterations 3.0369842E-03 5.9729397E-02 at 150iterations 1.7156765E-03 3.4118652E-02 at 160iterations 9.7556663E-04 1.9592285E-02 at 170iterations 5.5314542E-04 1.2367249E-02 at 180iterations finished qdiffx linear iterations at : 14:22:31 total time elapsed so far: 30.41000 # loops : 180 mean,max change (kT/e) : 5.5314542E-04 1.2367249E-02 energy calculations done at 30.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.58000 DelPhi exited at 14:22:37 30.583u 0.727s 0:37.89 82.6% 0+0k 0+0io 0pf+0w