Wed Dec 21 14:21:49 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+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 Wed Dec 21 2011 at 14:21:50 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6504421 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): -3.617000 48.51500 ymin,ymax (A): -4.999000 34.78500 zmin,zma (A): -23.52200 31.21000 x,y,z range (A): 52.13200 39.78400 54.73200 scale (grids/A): 0.6504421 object centre (A): 22.44900 14.89300 3.844001 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681010 assigned positive charge : 289.7500 centred at (gu) : 92.38593 89.42551 89.96459 assigned negative charge : -285.0693 centred at (gu) : 92.51157 89.29324 89.88420 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5669 nv = 96 ne = 84 npr = 40329 no. pairs analyzed = 40329 no. exposed pairs = 2482 no. arc points = 17498 no. surface atoms = 839 nbur = 1120 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 3143 m= 0 mr = 26 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1793 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7660847E-10 1.8430089E-08 midg,1,midg; midg,igrid,midg -6.2921104E-09 2.1514944E-08 1,midg,midg; igrid,midg,midg 1.4354934E-08 -8.4123588E-09 gauss-seidel spectral radius is 0.9876948 estimated iterations to convergence 74 setup time was (sec) 0.6300000 now iterating at: 14:21:52 rms-change max change #iterations 0.1319939 20.11621 at 10iterations 1.3316740E-02 1.904951 at 20iterations 1.3579489E-03 0.2069225 at 30iterations 1.4129555E-04 2.5909424E-02 at 40iterations 1.4425300E-05 2.6321411E-03 at 50iterations finished qdiffx linear iterations at : 14:21:56 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 1.4425300E-05 2.6321411E-03 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.790000 DelPhi exited at 14:22:03 4.795u 0.410s 0:12.98 40.0% 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 Wed Dec 21 2011 at 14:22:04 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.951326 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): -3.617000 48.51500 ymin,ymax (A): -4.999000 34.78500 zmin,zma (A): -23.52200 31.21000 x,y,z range (A): 52.13200 39.78400 54.73200 scale (grids/A): 1.951326 object centre (A): 22.44900 14.89300 3.844001 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681010 assigned positive charge : 289.7500 centred at (gu) : 97.15787 88.27660 89.89384 assigned negative charge : -285.0693 centred at (gu) : 97.53478 87.87974 89.65266 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 61077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17498 grid for indexing accessible points = 1.400000 m= 22161 mr = 42039 m= 3195 mr = 16731 m= 178 mr = 2055 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 25723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14439 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) : 0.6504421 object centre at (A) : 22.44900 14.89300 3.844001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4729400E-02 2.1952955E-02 midg,1,midg; midg,igrid,midg 3.2797677E-03 1.1728181E-02 1,midg,midg; igrid,midg,midg 3.3065796E-02 -4.1641579E-03 gauss-seidel spectral radius is 0.9986213 estimated iterations to convergence 213 setup time was (sec) 0.9500000 now iterating at: 14:22:06 rms-change max change #iterations 3.716249 161.2085 at 10iterations 1.730142 66.40347 at 20iterations 0.8104488 29.64855 at 30iterations 0.3771977 12.71160 at 40iterations 0.1757888 6.229877 at 50iterations 8.1803732E-02 2.629524 at 60iterations 3.8237460E-02 1.305661 at 70iterations 1.7856656E-02 0.5827942 at 80iterations 8.3148051E-03 0.2774761 at 90iterations 3.8790507E-03 0.1287694 at 100iterations 1.8067718E-03 5.8120728E-02 at 110iterations 8.4053451E-04 3.6428094E-02 at 120iterations finished qdiffx linear iterations at : 14:22:17 total time elapsed so far: 11.51000 # loops : 120 mean,max change (kT/e) : 8.4053451E-04 3.6428094E-02 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 14:22:21 11.699u 0.458s 0:17.43 69.6% 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 Wed Dec 21 2011 at 14:22:23 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.926990 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): -3.617000 48.51500 ymin,ymax (A): -4.999000 34.78500 zmin,zma (A): -23.52200 31.21000 x,y,z range (A): 52.13200 39.78400 54.73200 scale (grids/A): 2.926990 object centre (A): 22.44900 14.89300 3.844001 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681010 assigned positive charge : 289.7500 centred at (gu) : 100.7370 87.41492 89.84071 assigned negative charge : -285.0693 centred at (gu) : 101.3021 86.81975 89.47917 start vw surface at 0.1400000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 141062 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17498 grid for indexing accessible points = 1.400000 m= 71558 mr = 101680 m= 25651 mr = 59240 m= 5706 mr = 21035 m= 790 mr = 4344 m= 50 mr = 555 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 57939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 14608 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) : 1.951326 object centre at (A) : 22.44900 14.89300 3.844001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9353634 5.5727977E-02 midg,1,midg; midg,igrid,midg 8.6620010E-02 7.6520219E-02 1,midg,midg; igrid,midg,midg 0.2946259 -9.2288092E-02 gauss-seidel spectral radius is 0.9992425 estimated iterations to convergence 287 setup time was (sec) 1.860000 now iterating at: 14:22:26 rms-change max change #iterations 8.788277 384.2274 at 10iterations 5.083288 145.4454 at 20iterations 2.918920 67.19997 at 30iterations 1.670532 37.54982 at 40iterations 0.9552969 20.61447 at 50iterations 0.5454787 11.26125 at 60iterations 0.3122018 6.530899 at 70iterations 0.1782341 3.418165 at 80iterations 0.1014741 1.989843 at 90iterations 5.7974182E-02 1.138195 at 100iterations 3.2990880E-02 0.6877251 at 110iterations 1.8837217E-02 0.3822918 at 120iterations 1.0727486E-02 0.2105799 at 130iterations 6.1126333E-03 0.1232095 at 140iterations 3.4794533E-03 7.7510834E-02 at 150iterations 1.9873227E-03 3.9863586E-02 at 160iterations 1.1299825E-03 2.1807671E-02 at 170iterations 6.4476987E-04 1.2963295E-02 at 180iterations finished qdiffx linear iterations at : 14:22:43 total time elapsed so far: 18.70000 # loops : 180 mean,max change (kT/e) : 6.4476987E-04 1.2963295E-02 energy calculations done at 18.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.88000 DelPhi exited at 14:22:48 18.879u 0.505s 0:25.29 76.5% 0+0k 0+0io 0pf+0w