Mon Oct 10 13:57:04 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 Mon Oct 10 2011 at 13:57:04 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3325 !!! WARNING: SEP 90 has a net charge of -0.4750 !!! WARNING: GLM 146 has a net charge of -0.0940 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: 0.5636479 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): -20.91400 32.52100 ymin,ymax (A): -19.07100 31.02900 zmin,zma (A): -14.53000 48.63000 x,y,z range (A): 53.43500 50.10000 63.16000 scale (grids/A): 0.5636479 object centre (A): 5.803500 5.979000 17.05000 number of atom coordinates read : 3325 total number of charged atoms : 3182 net assigned charge : 1.431011 assigned positive charge : 511.8386 centred at (gu) : 90.23400 89.17583 90.85801 assigned negative charge : -510.4094 centred at (gu) : 90.38208 89.11526 90.76088 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6705 nv = 96 ne = 84 npr = 68727 no. pairs analyzed = 68727 no. exposed pairs = 3775 no. arc points = 26137 no. surface atoms = 1282 nbur = 2043 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 297 mr = 3791 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2741 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8823 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0080539E-09 1.9296957E-09 midg,1,midg; midg,igrid,midg -8.6598728E-10 8.5723845E-10 1,midg,midg; igrid,midg,midg 2.1531026E-09 -2.1219795E-09 gauss-seidel spectral radius is 0.9837801 estimated iterations to convergence 65 setup time was (sec) 0.6300000 now iterating at: 13:57:14 rms-change max change #iterations 8.8979036E-02 13.56915 at 10iterations 6.5311985E-03 0.9792194 at 20iterations 5.0764374E-04 7.5065613E-02 at 30iterations 4.1262163E-05 6.3018799E-03 at 40iterations 4.1568651E-06 6.3896179E-04 at 50iterations finished qdiffx linear iterations at : 13:57:18 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 4.1568651E-06 6.3896179E-04 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 13:57:19 4.546u 0.445s 0:14.40 34.5% 0+0k 0+0io 1pf+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 Mon Oct 10 2011 at 13:57:20 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3325 !!! WARNING: SEP 90 has a net charge of -0.4750 !!! WARNING: GLM 146 has a net charge of -0.0940 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: 1.690944 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): -20.91400 32.52100 ymin,ymax (A): -19.07100 31.02900 zmin,zma (A): -14.53000 48.63000 x,y,z range (A): 53.43500 50.10000 63.16000 scale (grids/A): 1.690944 object centre (A): 5.803500 5.979000 17.05000 number of atom coordinates read : 3325 total number of charged atoms : 3182 net assigned charge : 1.431011 assigned positive charge : 511.8386 centred at (gu) : 90.70094 87.52650 92.57297 assigned negative charge : -510.4094 centred at (gu) : 91.14599 87.34557 92.28235 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26137 grid for indexing accessible points = 1.400000 m= 24081 mr = 53694 m= 2827 mr = 17574 m= 101 mr = 1556 m= 0 mr = 22 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 609 time to turn everything in is 0.6000000 number of dielectric boundary points 29442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 24567 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) : 0.5636479 object centre at (A) : 5.803500 5.979000 17.05000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5466065E-02 1.7781002E-02 midg,1,midg; midg,igrid,midg -1.2740036E-02 1.3446697E-03 1,midg,midg; igrid,midg,midg 2.2773808E-02 -1.0637992E-02 gauss-seidel spectral radius is 0.9983370 estimated iterations to convergence 195 setup time was (sec) 0.9100000 now iterating at: 13:57:21 rms-change max change #iterations 3.848692 219.5576 at 10iterations 1.659354 61.08407 at 20iterations 0.7181243 26.97400 at 30iterations 0.3135270 10.38617 at 40iterations 0.1362225 4.446540 at 50iterations 5.9057567E-02 2.019315 at 60iterations 2.5578659E-02 0.8427124 at 70iterations 1.1073812E-02 0.3431273 at 80iterations 4.8086555E-03 0.1715117 at 90iterations 2.0939256E-03 7.4213505E-02 at 100iterations 9.0828200E-04 2.9232025E-02 at 110iterations 3.9464814E-04 1.3829231E-02 at 120iterations finished qdiffx linear iterations at : 13:57:32 total time elapsed so far: 11.50000 # loops : 120 mean,max change (kT/e) : 3.9464814E-04 1.3829231E-02 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.67000 DelPhi exited at 13:57:33 11.675u 0.574s 0:13.69 89.4% 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 Mon Oct 10 2011 at 13:57:33 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3325 !!! WARNING: SEP 90 has a net charge of -0.4750 !!! WARNING: GLM 146 has a net charge of -0.0940 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: 2.536416 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): -20.91400 32.52100 ymin,ymax (A): -19.07100 31.02900 zmin,zma (A): -14.53000 48.63000 x,y,z range (A): 53.43500 50.10000 63.16000 scale (grids/A): 2.536416 object centre (A): 5.803500 5.979000 17.05000 number of atom coordinates read : 3325 total number of charged atoms : 3182 net assigned charge : 1.431011 assigned positive charge : 511.8386 centred at (gu) : 91.05118 86.28955 93.85926 assigned negative charge : -510.4094 centred at (gu) : 91.71893 86.01847 93.42355 start vw surface at 0.1400000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 175668 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26137 grid for indexing accessible points = 1.400000 m= 83189 mr = 131302 m= 24825 mr = 68072 m= 4590 mr = 19421 m= 396 mr = 3171 m= 13 mr = 246 m= 0 mr = 2 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1964 time to turn everything in is 1.550000 number of dielectric boundary points 66467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 25441 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) : 1.690944 object centre at (A) : 5.803500 5.979000 17.05000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4499692 0.3596079 midg,1,midg; midg,igrid,midg -0.1869460 5.0072230E-02 1,midg,midg; igrid,midg,midg 0.4006132 -0.1666042 gauss-seidel spectral radius is 0.9991834 estimated iterations to convergence 276 setup time was (sec) 1.930000 now iterating at: 13:57:36 rms-change max change #iterations 9.613217 268.5556 at 10iterations 5.395423 109.0314 at 20iterations 3.032523 66.31300 at 30iterations 1.697955 33.23996 at 40iterations 0.9514462 17.00761 at 50iterations 0.5322877 9.521751 at 60iterations 0.2967675 5.623506 at 70iterations 0.1658386 2.943482 at 80iterations 9.2526875E-02 1.919935 at 90iterations 5.1671106E-02 0.9973373 at 100iterations 2.8891522E-02 0.5683028 at 110iterations 1.6119758E-02 0.3129647 at 120iterations 8.9981044E-03 0.1643105 at 130iterations 5.0273403E-03 0.1020913 at 140iterations 2.8091678E-03 5.2099228E-02 at 150iterations 1.5694704E-03 2.9064178E-02 at 160iterations 8.7712996E-04 1.6102314E-02 at 170iterations 4.9056788E-04 9.5057487E-03 at 180iterations finished qdiffx linear iterations at : 13:57:56 total time elapsed so far: 21.82000 # loops : 180 mean,max change (kT/e) : 4.9056788E-04 9.5057487E-03 energy calculations done at 21.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.99000 DelPhi exited at 13:57:56 21.992u 0.629s 0:23.09 97.9% 0+0k 0+0io 0pf+0w