Mon Oct 10 09:24:16 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 09:24:16 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6389088 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): -5.315000 34.73500 ymin,ymax (A): -3.683000 48.18700 zmin,zma (A): -24.43400 31.28600 x,y,z range (A): 40.05000 51.87000 55.72000 scale (grids/A): 0.6389088 object centre (A): 14.71000 22.25200 3.426001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 90.69302 92.59779 90.14336 assigned negative charge : -288.4263 centred at (gu) : 90.79825 92.73294 90.09187 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5486 nv = 96 ne = 84 npr = 40400 no. pairs analyzed = 40400 no. exposed pairs = 2475 no. arc points = 17574 no. surface atoms = 834 nbur = 1130 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 3054 m= 0 mr = 44 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2500000 number of dielectric boundary points 2698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1816 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6552 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8490998E-10 9.1486108E-09 midg,1,midg; midg,igrid,midg 9.0578984E-09 -1.2411912E-08 1,midg,midg; igrid,midg,midg 1.1448899E-08 -5.0135416E-09 gauss-seidel spectral radius is 0.9872532 estimated iterations to convergence 72 setup time was (sec) 0.4700000 now iterating at: 09:24:17 rms-change max change #iterations 0.1261682 20.59204 at 10iterations 1.2471545E-02 1.979416 at 20iterations 1.2189411E-03 0.2018145 at 30iterations 1.2092601E-04 1.8265247E-02 at 40iterations 1.1879069E-05 2.0742416E-03 at 50iterations finished qdiffx linear iterations at : 09:24:19 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.1879069E-05 2.0742416E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 09:24:20 3.254u 0.170s 0:03.73 91.6% 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 Mon Oct 10 2011 at 09:24:20 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.916726 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): -5.315000 34.73500 ymin,ymax (A): -3.683000 48.18700 zmin,zma (A): -24.43400 31.28600 x,y,z range (A): 40.05000 51.87000 55.72000 scale (grids/A): 1.916726 object centre (A): 14.71000 22.25200 3.426001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 92.07912 97.79369 90.43002 assigned negative charge : -288.4263 centred at (gu) : 92.39487 98.19896 90.27562 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 58720 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17574 grid for indexing accessible points = 1.400000 m= 22399 mr = 40438 m= 3645 mr = 17091 m= 214 mr = 2454 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1151 time to turn everything in is 0.4300000 number of dielectric boundary points 24929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14427 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) : 0.6389088 object centre at (A) : 14.71000 22.25200 3.426001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4591513E-02 1.3089837E-02 midg,1,midg; midg,igrid,midg 3.0769240E-02 -8.1922514E-03 1,midg,midg; igrid,midg,midg 8.5312324E-03 -5.4516019E-03 gauss-seidel spectral radius is 0.9985749 estimated iterations to convergence 210 setup time was (sec) 0.7100000 now iterating at: 09:24:21 rms-change max change #iterations 3.657297 174.3651 at 10iterations 1.685029 60.98477 at 20iterations 0.7770308 31.16279 at 30iterations 0.3585521 13.10263 at 40iterations 0.1648442 5.544678 at 50iterations 7.5654075E-02 2.622202 at 60iterations 3.4698825E-02 1.194448 at 70iterations 1.5999440E-02 0.5313797 at 80iterations 7.4025160E-03 0.2839508 at 90iterations 3.4019072E-03 0.1282454 at 100iterations 1.5682578E-03 4.9890995E-02 at 110iterations 7.1949005E-04 2.3290634E-02 at 120iterations finished qdiffx linear iterations at : 09:24:28 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 7.1949005E-04 2.3290634E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 09:24:28 7.796u 0.231s 0:08.50 94.3% 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 09:24:28 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.875090 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): -5.315000 34.73500 ymin,ymax (A): -3.683000 48.18700 zmin,zma (A): -24.43400 31.28600 x,y,z range (A): 40.05000 51.87000 55.72000 scale (grids/A): 2.875090 object centre (A): 14.71000 22.25200 3.426001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 93.11880 101.6904 90.64517 assigned negative charge : -288.4263 centred at (gu) : 93.59231 102.2986 90.41354 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 135551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17574 grid for indexing accessible points = 1.400000 m= 70381 mr = 97567 m= 27350 mr = 58474 m= 6765 mr = 22842 m= 917 mr = 5292 m= 47 mr = 620 m= 0 mr = 27 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 3537 time to turn everything in is 1.070000 number of dielectric boundary points 56189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 14656 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) : 1.916726 object centre at (A) : 14.71000 22.25200 3.426001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.054392 7.2578145E-03 midg,1,midg; midg,igrid,midg 0.3348089 -0.1199768 1,midg,midg; igrid,midg,midg 4.7877207E-02 -3.4621712E-02 gauss-seidel spectral radius is 0.9992298 estimated iterations to convergence 284 setup time was (sec) 1.370000 now iterating at: 09:24:30 rms-change max change #iterations 8.615420 530.1027 at 10iterations 4.936759 112.6239 at 20iterations 2.808763 67.35229 at 30iterations 1.593218 34.91365 at 40iterations 0.9046386 19.86099 at 50iterations 0.5143975 10.37679 at 60iterations 0.2910273 5.493233 at 70iterations 0.1650251 3.399773 at 80iterations 9.3535006E-02 2.005371 at 90iterations 5.3124048E-02 1.023350 at 100iterations 3.0081719E-02 0.6153588 at 110iterations 1.7021911E-02 0.3585052 at 120iterations 9.6727079E-03 0.2019353 at 130iterations 5.4700240E-03 0.1136022 at 140iterations 3.1030865E-03 6.5053940E-02 at 150iterations 1.7579151E-03 3.5921574E-02 at 160iterations 9.9529279E-04 1.9764900E-02 at 170iterations 5.6472112E-04 1.0900497E-02 at 180iterations finished qdiffx linear iterations at : 09:24:40 total time elapsed so far: 11.42000 # loops : 180 mean,max change (kT/e) : 5.6472112E-04 1.0900497E-02 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 09:24:40 11.588u 0.219s 0:12.08 97.5% 0+0k 0+0io 0pf+0w