Sun Oct 9 14:05:38 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 Sun Oct 9 2011 at 14:05:38 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 = 2355 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: 0.6993968 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): -13.75300 35.65100 ymin,ymax (A): -0.6240000 50.27700 zmin,zma (A): 1.587000 44.84900 x,y,z range (A): 49.40400 50.90100 43.26200 scale (grids/A): 0.6993968 object centre (A): 10.94900 24.82650 23.21800 number of atom coordinates read : 2355 total number of charged atoms : 2214 net assigned charge : 3.500020 assigned positive charge : 359.2311 centred at (gu) : 89.47189 88.67901 90.80099 assigned negative charge : -355.7316 centred at (gu) : 89.43971 88.49145 90.86552 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7812 nv = 96 ne = 84 npr = 47200 no. pairs analyzed = 47200 no. exposed pairs = 2934 no. arc points = 20375 no. surface atoms = 990 nbur = 1365 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 506 mr = 4413 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.2000000 number of dielectric boundary points 3827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1868 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8786 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7985253E-08 -5.4146234E-09 midg,1,midg; midg,igrid,midg -8.3654371E-08 8.6558423E-08 1,midg,midg; igrid,midg,midg 1.2009838E-08 3.7101216E-08 gauss-seidel spectral radius is 0.9893754 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 14:05:38 rms-change max change #iterations 0.2014299 30.55264 at 10iterations 2.4835033E-02 3.324577 at 20iterations 3.3710999E-03 0.4864349 at 30iterations 6.8377145E-04 0.1157894 at 40iterations 2.1172114E-04 3.5514832E-02 at 50iterations finished qdiffx linear iterations at : 14:05:41 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.1172114E-04 3.5514832E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:05:42 3.441u 0.155s 0:03.88 92.5% 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 Sun Oct 9 2011 at 14:05:42 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 = 2355 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: 2.098191 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): -13.75300 35.65100 ymin,ymax (A): -0.6240000 50.27700 zmin,zma (A): 1.587000 44.84900 x,y,z range (A): 49.40400 50.90100 43.26200 scale (grids/A): 2.098191 object centre (A): 10.94900 24.82650 23.21800 number of atom coordinates read : 2355 total number of charged atoms : 2214 net assigned charge : 3.500020 assigned positive charge : 359.2311 centred at (gu) : 88.41537 86.03652 92.40252 assigned negative charge : -355.7316 centred at (gu) : 88.31897 85.47421 92.59634 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20375 grid for indexing accessible points = 1.400000 m= 32841 mr = 58052 m= 6102 mr = 24667 m= 539 mr = 3972 m= 12 mr = 255 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.4100000 number of dielectric boundary points 35425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17565 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) : 0.6993968 object centre at (A) : 10.94900 24.82650 23.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7674611E-02 6.4741378E-04 midg,1,midg; midg,igrid,midg -5.1811699E-02 1.6523207E-02 1,midg,midg; igrid,midg,midg -1.6884269E-02 5.9512239E-02 gauss-seidel spectral radius is 0.9988400 estimated iterations to convergence 232 setup time was (sec) 0.6200000 now iterating at: 14:05:42 rms-change max change #iterations 4.871777 215.9471 at 10iterations 2.414699 81.59560 at 20iterations 1.194568 38.60857 at 30iterations 0.5931276 19.76509 at 40iterations 0.2955722 9.471386 at 50iterations 0.1467662 4.516505 at 60iterations 7.3336072E-02 2.072693 at 70iterations 3.6497403E-02 1.044424 at 80iterations 1.8370001E-02 0.6103821 at 90iterations 9.2505040E-03 0.2560425 at 100iterations 4.7396724E-03 0.1465149 at 110iterations 2.5016349E-03 7.8723907E-02 at 120iterations finished qdiffx linear iterations at : 14:05:50 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.5016349E-03 7.8723907E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 14:05:50 7.945u 0.211s 0:08.42 96.7% 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 Sun Oct 9 2011 at 14:05:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2355 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: 3.147286 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): -13.75300 35.65100 ymin,ymax (A): -0.6240000 50.27700 zmin,zma (A): 1.587000 44.84900 x,y,z range (A): 49.40400 50.90100 43.26200 scale (grids/A): 3.147286 object centre (A): 10.94900 24.82650 23.21800 number of atom coordinates read : 2355 total number of charged atoms : 2214 net assigned charge : 3.500020 assigned positive charge : 359.2311 centred at (gu) : 87.62309 84.05463 93.60370 assigned negative charge : -355.7316 centred at (gu) : 87.47834 83.21130 93.89438 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 191155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20375 grid for indexing accessible points = 1.400000 m= 101925 mr = 139955 m= 40967 mr = 84274 m= 11441 mr = 33357 m= 2167 mr = 8688 m= 199 mr = 1563 m= 5 mr = 90 m= 0 mr = 2 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 1.260000 number of dielectric boundary points 79930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 17704 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) : 2.098191 object centre at (A) : 10.94900 24.82650 23.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4705423 -0.1042643 midg,1,midg; midg,igrid,midg -0.5508569 0.2933575 1,midg,midg; igrid,midg,midg -0.6054771 0.5808990 gauss-seidel spectral radius is 0.9993030 estimated iterations to convergence 299 setup time was (sec) 1.510000 now iterating at: 14:05:52 rms-change max change #iterations 11.03785 361.0477 at 10iterations 6.614126 171.0077 at 20iterations 3.957136 75.67758 at 30iterations 2.346200 45.44583 at 40iterations 1.394152 23.59172 at 50iterations 0.8222989 12.94245 at 60iterations 0.4866438 8.682563 at 70iterations 0.2871209 5.091934 at 80iterations 0.1686411 2.720407 at 90iterations 9.9425897E-02 1.753296 at 100iterations 5.8440827E-02 1.036146 at 110iterations 3.4476750E-02 0.6201501 at 120iterations 2.0459004E-02 0.3517799 at 130iterations 1.2251633E-02 0.2226553 at 140iterations 7.5141103E-03 0.1365433 at 150iterations 4.7709229E-03 9.9906921E-02 at 160iterations 3.1862510E-03 6.8866730E-02 at 170iterations 2.2694422E-03 4.9503326E-02 at 180iterations finished qdiffx linear iterations at : 14:06:03 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 2.2694422E-03 4.9503326E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 14:06:04 13.098u 0.215s 0:13.58 97.9% 0+0k 0+0io 0pf+0w