Tue Oct 11 08:08:16 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+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 Tue Oct 11 2011 at 08:08:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2308 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: 0.6400231 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): -22.73100 29.11900 ymin,ymax (A): 22.10200 77.72500 zmin,zma (A): 2.230000 51.79900 x,y,z range (A): 51.85000 55.62300 49.56900 scale (grids/A): 0.6400231 object centre (A): 3.194000 49.91350 27.01450 number of atom coordinates read : 2308 total number of charged atoms : 2172 net assigned charge : 7.500029 assigned positive charge : 346.6903 centred at (gu) : 90.34341 87.71972 92.05122 assigned negative charge : -339.1909 centred at (gu) : 90.22124 87.69322 91.99445 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6425 nv = 96 ne = 84 npr = 45939 no. pairs analyzed = 45939 no. exposed pairs = 3082 no. arc points = 21716 no. surface atoms = 1030 nbur = 1278 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 3319 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2198 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7672 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3460887E-09 2.5395813E-08 midg,1,midg; midg,igrid,midg 1.2810551E-08 8.3658236E-09 1,midg,midg; igrid,midg,midg -1.6155211E-09 2.4613446E-08 gauss-seidel spectral radius is 0.9873320 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 08:08:17 rms-change max change #iterations 0.1338812 26.69918 at 10iterations 1.3248490E-02 1.916973 at 20iterations 1.3571730E-03 0.2046127 at 30iterations 1.6056022E-04 3.1323433E-02 at 40iterations 3.7050635E-05 8.1062317E-03 at 50iterations finished qdiffx linear iterations at : 08:08:20 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 3.7050635E-05 8.1062317E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 08:08:21 4.016u 0.289s 0:04.86 88.2% 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 Tue Oct 11 2011 at 08:08:21 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 = 2308 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: 1.920069 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): -22.73100 29.11900 ymin,ymax (A): 22.10200 77.72500 zmin,zma (A): 2.230000 51.79900 x,y,z range (A): 51.85000 55.62300 49.56900 scale (grids/A): 1.920069 object centre (A): 3.194000 49.91350 27.01450 number of atom coordinates read : 2308 total number of charged atoms : 2172 net assigned charge : 7.500029 assigned positive charge : 346.6903 centred at (gu) : 91.03004 83.15887 96.15331 assigned negative charge : -339.1909 centred at (gu) : 90.66364 83.07952 95.98342 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69711 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21716 grid for indexing accessible points = 1.400000 m= 24337 mr = 47003 m= 3704 mr = 17243 m= 224 mr = 2070 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 31577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17134 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) : 0.6400231 object centre at (A) : 3.194000 49.91350 27.01450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0324889E-03 3.5752572E-02 midg,1,midg; midg,igrid,midg 5.3240106E-02 4.6622440E-02 1,midg,midg; igrid,midg,midg -5.9056263E-03 2.9666109E-02 gauss-seidel spectral radius is 0.9986254 estimated iterations to convergence 214 setup time was (sec) 0.9200000 now iterating at: 08:08:22 rms-change max change #iterations 3.987360 175.5771 at 10iterations 1.859199 67.47192 at 20iterations 0.8635974 26.93822 at 30iterations 0.4036494 14.72292 at 40iterations 0.1883767 6.164412 at 50iterations 8.7759018E-02 3.101757 at 60iterations 4.0997744E-02 1.391563 at 70iterations 1.9117070E-02 0.6806026 at 80iterations 8.9326967E-03 0.3046184 at 90iterations 4.1602915E-03 0.1442614 at 100iterations 1.9548975E-03 6.1084747E-02 at 110iterations 9.2541258E-04 3.1368256E-02 at 120iterations finished qdiffx linear iterations at : 08:08:31 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 9.2541258E-04 3.1368256E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 08:08:31 9.371u 0.299s 0:10.28 93.9% 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 Tue Oct 11 2011 at 08:08:31 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 = 2308 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: 2.880104 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): -22.73100 29.11900 ymin,ymax (A): 22.10200 77.72500 zmin,zma (A): 2.230000 51.79900 x,y,z range (A): 51.85000 55.62300 49.56900 scale (grids/A): 2.880104 object centre (A): 3.194000 49.91350 27.01450 number of atom coordinates read : 2308 total number of charged atoms : 2172 net assigned charge : 7.500029 assigned positive charge : 346.6903 centred at (gu) : 91.54487 79.73814 99.22994 assigned negative charge : -339.1909 centred at (gu) : 90.99551 79.61933 98.97502 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 160887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21716 grid for indexing accessible points = 1.400000 m= 79175 mr = 114148 m= 27763 mr = 63339 m= 6455 mr = 21550 m= 950 mr = 4461 m= 69 mr = 582 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.610000 number of dielectric boundary points 71185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 17375 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) : 1.920069 object centre at (A) : 3.194000 49.91350 27.01450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1516150E-02 0.3384482 midg,1,midg; midg,igrid,midg 0.4848091 0.7502143 1,midg,midg; igrid,midg,midg -3.3461146E-02 0.4673621 gauss-seidel spectral radius is 0.9992611 estimated iterations to convergence 290 setup time was (sec) 1.940000 now iterating at: 08:08:34 rms-change max change #iterations 9.563433 474.9397 at 10iterations 5.651281 135.7570 at 20iterations 3.307431 77.44506 at 30iterations 1.925049 44.16203 at 40iterations 1.118287 26.32631 at 50iterations 0.6484739 16.16446 at 60iterations 0.3754088 10.43393 at 70iterations 0.2171408 4.451302 at 80iterations 0.1250948 2.390654 at 90iterations 7.2185814E-02 1.333264 at 100iterations 4.1444786E-02 0.7654629 at 110iterations 2.3946503E-02 0.4503825 at 120iterations 1.3759270E-02 0.2866116 at 130iterations 7.9444693E-03 0.1556396 at 140iterations 4.5902049E-03 8.5193634E-02 at 150iterations 2.6568379E-03 5.7369232E-02 at 160iterations 1.5484146E-03 3.1450272E-02 at 170iterations 9.1606739E-04 1.9355774E-02 at 180iterations finished qdiffx linear iterations at : 08:08:47 total time elapsed so far: 15.53000 # loops : 180 mean,max change (kT/e) : 9.1606739E-04 1.9355774E-02 energy calculations done at 15.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.71000 DelPhi exited at 08:08:48 15.708u 0.310s 0:16.52 96.9% 0+0k 0+0io 0pf+0w