Wed Dec 28 11:03:02 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 28 2011 at 11:03:02 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6523970 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): -5.239000 35.05400 ymin,ymax (A): -3.450000 49.47000 zmin,zma (A): -7.713000 46.85500 x,y,z range (A): 40.29300 52.92000 54.56800 scale (grids/A): 0.6523970 object centre (A): 14.90750 23.01000 19.57100 number of atom coordinates read : 1957 total number of charged atoms : 1824 net assigned charge : 4.681008 assigned positive charge : 286.9481 centred at (gu) : 89.30980 92.17558 89.96172 assigned negative charge : -282.2673 centred at (gu) : 89.20625 92.31194 90.02980 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5785 nv = 96 ne = 84 npr = 39676 no. pairs analyzed = 39676 no. exposed pairs = 2571 no. arc points = 18056 no. surface atoms = 872 nbur = 1085 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 260 mr = 3128 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1849 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6657 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8196525E-08 2.0526474E-09 midg,1,midg; midg,igrid,midg 1.6493527E-08 -1.0249869E-08 1,midg,midg; igrid,midg,midg -2.6181994E-09 1.9173411E-08 gauss-seidel spectral radius is 0.9877706 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 11:03:03 rms-change max change #iterations 0.1293423 21.33291 at 10iterations 1.3157814E-02 2.142387 at 20iterations 1.3516663E-03 0.2155905 at 30iterations 1.3684189E-04 2.1766663E-02 at 40iterations 1.4438304E-05 2.0942688E-03 at 50iterations finished qdiffx linear iterations at : 11:03:06 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 1.4438304E-05 2.0942688E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 11:03:07 4.079u 0.174s 0:04.87 87.0% 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 28 2011 at 11:03:07 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.957191 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): -5.239000 35.05400 ymin,ymax (A): -3.450000 49.47000 zmin,zma (A): -7.713000 46.85500 x,y,z range (A): 40.29300 52.92000 54.56800 scale (grids/A): 1.957191 object centre (A): 14.90750 23.01000 19.57100 number of atom coordinates read : 1957 total number of charged atoms : 1824 net assigned charge : 4.681008 assigned positive charge : 286.9481 centred at (gu) : 87.92976 96.52687 89.88525 assigned negative charge : -282.2673 centred at (gu) : 87.61891 96.93618 90.08958 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 61984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18056 grid for indexing accessible points = 1.400000 m= 22849 mr = 42297 m= 3421 mr = 17116 m= 207 mr = 2135 m= 1 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 301 time to turn everything in is 0.6400000 number of dielectric boundary points 26835 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14400 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) : 0.6523970 object centre at (A) : 14.90750 23.01000 19.57100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4543638E-02 2.8464869E-02 midg,1,midg; midg,igrid,midg 4.1650631E-02 -7.0471037E-03 1,midg,midg; igrid,midg,midg 5.0477055E-03 1.1794816E-02 gauss-seidel spectral radius is 0.9986346 estimated iterations to convergence 214 setup time was (sec) 0.9900000 now iterating at: 11:03:08 rms-change max change #iterations 3.705631 182.1885 at 10iterations 1.739017 67.55399 at 20iterations 0.8116676 27.49361 at 30iterations 0.3794333 13.02169 at 40iterations 0.1770787 6.800140 at 50iterations 8.2954384E-02 2.813585 at 60iterations 3.8827199E-02 1.393841 at 70iterations 1.8185752E-02 0.6907454 at 80iterations 8.4835356E-03 0.3159897 at 90iterations 3.9721159E-03 0.1297066 at 100iterations 1.8623578E-03 6.8054199E-02 at 110iterations 8.7058474E-04 3.0451149E-02 at 120iterations finished qdiffx linear iterations at : 11:03:17 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 8.7058474E-04 3.0451149E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 11:03:18 9.646u 0.243s 0:10.46 94.4% 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 28 2011 at 11:03:18 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.935786 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): -5.239000 35.05400 ymin,ymax (A): -3.450000 49.47000 zmin,zma (A): -7.713000 46.85500 x,y,z range (A): 40.29300 52.92000 54.56800 scale (grids/A): 2.935786 object centre (A): 14.90750 23.01000 19.57100 number of atom coordinates read : 1957 total number of charged atoms : 1824 net assigned charge : 4.681008 assigned positive charge : 286.9481 centred at (gu) : 86.89471 99.79040 89.82790 assigned negative charge : -282.2673 centred at (gu) : 86.42848 100.4043 90.13441 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 143198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18056 grid for indexing accessible points = 1.400000 m= 73350 mr = 102276 m= 26825 mr = 60526 m= 5992 mr = 21883 m= 808 mr = 4448 m= 44 mr = 521 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1032 time to turn everything in is 1.540000 number of dielectric boundary points 60547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 14592 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) : 1.957191 object centre at (A) : 14.90750 23.01000 19.57100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2313011E-02 0.7547777 midg,1,midg; midg,igrid,midg 0.4468074 -0.1228170 1,midg,midg; igrid,midg,midg 9.9445090E-02 7.9942413E-02 gauss-seidel spectral radius is 0.9992497 estimated iterations to convergence 288 setup time was (sec) 1.900000 now iterating at: 11:03:20 rms-change max change #iterations 8.801961 531.4454 at 10iterations 5.148164 136.7001 at 20iterations 2.968027 72.62556 at 30iterations 1.718711 36.88990 at 40iterations 0.9873391 20.33042 at 50iterations 0.5678769 11.99147 at 60iterations 0.3263713 6.676807 at 70iterations 0.1868445 3.652145 at 80iterations 0.1069375 2.036385 at 90iterations 6.1331008E-02 1.219487 at 100iterations 3.5029277E-02 0.7696344 at 110iterations 2.0075049E-02 0.3918025 at 120iterations 1.1455247E-02 0.2185669 at 130iterations 6.5497118E-03 0.1503847 at 140iterations 3.7453976E-03 7.0771813E-02 at 150iterations 2.1396175E-03 4.4347763E-02 at 160iterations 1.2252470E-03 2.2811890E-02 at 170iterations 6.9850549E-04 1.2956619E-02 at 180iterations finished qdiffx linear iterations at : 11:03:32 total time elapsed so far: 14.15000 # loops : 180 mean,max change (kT/e) : 6.9850549E-04 1.2956619E-02 energy calculations done at 14.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.42000 DelPhi exited at 11:03:33 14.418u 0.255s 0:15.75 93.0% 0+0k 0+0io 0pf+0w