Sat Oct 15 12:08:06 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+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 Sat Oct 15 2011 at 12:08:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2255 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: 0.6618946 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): -0.4250001 53.36000 ymin,ymax (A): -16.16100 27.56100 zmin,zma (A): 32.69300 84.57899 x,y,z range (A): 53.78500 43.72200 51.88600 scale (grids/A): 0.6618946 object centre (A): 26.46750 5.700001 58.63599 number of atom coordinates read : 2255 total number of charged atoms : 2122 net assigned charge : 13.00001 assigned positive charge : 328.5715 centred at (gu) : 90.51109 89.42719 88.65498 assigned negative charge : -315.5722 centred at (gu) : 90.50964 89.43859 88.75060 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6886 nv = 96 ne = 84 npr = 44600 no. pairs analyzed = 44600 no. exposed pairs = 3027 no. arc points = 21434 no. surface atoms = 1010 nbur = 1245 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 3638 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 90 time to turn everything in is 0.1800000 number of dielectric boundary points 3626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2035 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6445594E-08 1.4114738E-08 midg,1,midg; midg,igrid,midg 4.0817756E-08 2.9031961E-08 1,midg,midg; igrid,midg,midg 3.0897379E-08 3.8444366E-08 gauss-seidel spectral radius is 0.9881466 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 12:08:07 rms-change max change #iterations 0.1524469 21.75054 at 10iterations 1.6382264E-02 2.342937 at 20iterations 2.0253086E-03 0.2823277 at 30iterations 4.3852665E-04 6.4529419E-02 at 40iterations 1.4708620E-04 2.1436691E-02 at 50iterations finished qdiffx linear iterations at : 12:08:10 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 1.4708620E-04 2.1436691E-02 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 12:08:11 3.747u 0.229s 0:04.40 90.0% 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 Sat Oct 15 2011 at 12:08:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2255 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: 1.985684 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): -0.4250001 53.36000 ymin,ymax (A): -16.16100 27.56100 zmin,zma (A): 32.69300 84.57899 x,y,z range (A): 53.78500 43.72200 51.88600 scale (grids/A): 1.985684 object centre (A): 26.46750 5.700001 58.63599 number of atom coordinates read : 2255 total number of charged atoms : 2122 net assigned charge : 13.00001 assigned positive charge : 328.5715 centred at (gu) : 91.53287 88.28133 85.96481 assigned negative charge : -315.5722 centred at (gu) : 91.52907 88.31589 86.25183 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21434 grid for indexing accessible points = 1.400000 m= 27118 mr = 49487 m= 4880 mr = 19416 m= 408 mr = 3075 m= 4 mr = 151 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2008 time to turn everything in is 0.3600000 number of dielectric boundary points 33257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 16785 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) : 0.6618946 object centre at (A) : 26.46750 5.700001 58.63599 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4212693E-02 4.6826106E-02 midg,1,midg; midg,igrid,midg 3.2041214E-02 1.1001691E-02 1,midg,midg; igrid,midg,midg 4.7279682E-02 5.2914929E-02 gauss-seidel spectral radius is 0.9987157 estimated iterations to convergence 221 setup time was (sec) 0.5800000 now iterating at: 12:08:12 rms-change max change #iterations 4.144651 203.9635 at 10iterations 1.984700 68.03843 at 20iterations 0.9495189 35.35962 at 30iterations 0.4535628 14.47123 at 40iterations 0.2180089 7.036980 at 50iterations 0.1040635 3.264852 at 60iterations 5.0156843E-02 1.604759 at 70iterations 2.3970803E-02 0.7972002 at 80iterations 1.1643587E-02 0.3598111 at 90iterations 5.7163136E-03 0.1828613 at 100iterations 2.8773302E-03 0.1021776 at 110iterations 1.5284970E-03 5.2425385E-02 at 120iterations finished qdiffx linear iterations at : 12:08:19 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 1.5284970E-03 5.2425385E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 12:08:20 8.160u 0.257s 0:08.76 96.0% 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 Sat Oct 15 2011 at 12:08:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2255 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: 2.978526 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): -0.4250001 53.36000 ymin,ymax (A): -16.16100 27.56100 zmin,zma (A): 32.69300 84.57899 x,y,z range (A): 53.78500 43.72200 51.88600 scale (grids/A): 2.978526 object centre (A): 26.46750 5.700001 58.63599 number of atom coordinates read : 2255 total number of charged atoms : 2122 net assigned charge : 13.00001 assigned positive charge : 328.5715 centred at (gu) : 92.29939 87.42197 83.94714 assigned negative charge : -315.5722 centred at (gu) : 92.29375 87.47385 84.37789 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 168284 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21434 grid for indexing accessible points = 1.400000 m= 85631 mr = 119833 m= 32864 mr = 68720 m= 9048 mr = 26095 m= 1597 mr = 6684 m= 145 mr = 1092 m= 3 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 6495 time to turn everything in is 1.020000 number of dielectric boundary points 75086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 16976 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) : 1.985684 object centre at (A) : 26.46750 5.700001 58.63599 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8900481 0.6362885 midg,1,midg; midg,igrid,midg 0.2826049 5.2561440E-02 1,midg,midg; igrid,midg,midg 0.4456415 0.4327331 gauss-seidel spectral radius is 0.9992830 estimated iterations to convergence 295 setup time was (sec) 1.270000 now iterating at: 12:08:21 rms-change max change #iterations 9.673262 378.2679 at 10iterations 5.754715 125.3666 at 20iterations 3.407377 68.48312 at 30iterations 1.999336 39.79146 at 40iterations 1.177575 23.70848 at 50iterations 0.6878945 14.36991 at 60iterations 0.4027380 8.218579 at 70iterations 0.2351283 4.538287 at 80iterations 0.1372969 2.705694 at 90iterations 8.0145322E-02 1.476649 at 100iterations 4.6511486E-02 0.8396621 at 110iterations 2.7160889E-02 0.5528898 at 120iterations 1.5824081E-02 0.2911510 at 130iterations 9.2409085E-03 0.1887622 at 140iterations 5.4369373E-03 0.1085567 at 150iterations 3.2274439E-03 6.0350418E-02 at 160iterations 1.9540396E-03 3.9039612E-02 at 170iterations 1.2310229E-03 2.5550842E-02 at 180iterations finished qdiffx linear iterations at : 12:08:39 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 1.2310229E-03 2.5550842E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 12:08:40 13.263u 0.345s 0:20.45 66.5% 0+0k 0+0io 0pf+0w