Sat Oct 8 20:33:00 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 Sat Oct 8 2011 at 20:33:00 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 0.6192920 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): -31.33300 17.51400 ymin,ymax (A): -23.56500 23.05300 zmin,zma (A): -12.48900 44.99600 x,y,z range (A): 48.84700 46.61800 57.48500 scale (grids/A): 0.6192920 object centre (A): -6.909500 -0.2560005 16.25350 number of atom coordinates read : 2605 total number of charged atoms : 2462 net assigned charge : 4.406006 assigned positive charge : 394.2350 centred at (gu) : 88.50969 89.14900 89.59001 assigned negative charge : -389.8296 centred at (gu) : 88.41090 89.20950 89.47445 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6449 nv = 96 ne = 84 npr = 54825 no. pairs analyzed = 54825 no. exposed pairs = 3017 no. arc points = 21554 no. surface atoms = 1017 nbur = 1588 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3574 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2900000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2138 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4683932E-09 1.0058518E-08 midg,1,midg; midg,igrid,midg 9.0372092E-09 -2.9840086E-10 1,midg,midg; igrid,midg,midg -4.2071577E-09 7.1782154E-09 gauss-seidel spectral radius is 0.9864927 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 20:33:01 rms-change max change #iterations 0.1252134 21.95713 at 10iterations 1.1666813E-02 1.635647 at 20iterations 1.0706980E-03 0.1887759 at 30iterations 1.0147349E-04 1.3219833E-02 at 40iterations 9.5590258E-06 1.7280579E-03 at 50iterations finished qdiffx linear iterations at : 20:33:04 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 9.5590258E-06 1.7280579E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 20:33:04 3.325u 0.213s 0:03.81 92.6% 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 Sat Oct 8 2011 at 20:33:04 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 1.857876 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): -31.33300 17.51400 ymin,ymax (A): -23.56500 23.05300 zmin,zma (A): -12.48900 44.99600 x,y,z range (A): 48.84700 46.61800 57.48500 scale (grids/A): 1.857876 object centre (A): -6.909500 -0.2560005 16.25350 number of atom coordinates read : 2605 total number of charged atoms : 2462 net assigned charge : 4.406006 assigned positive charge : 394.2350 centred at (gu) : 85.52853 87.44696 88.76960 assigned negative charge : -389.8296 centred at (gu) : 85.23246 87.62841 88.42303 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21554 grid for indexing accessible points = 1.400000 m= 23763 mr = 48504 m= 3388 mr = 17472 m= 195 mr = 1983 m= 7 mr = 65 m= 1 mr = 0 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3182 time to turn everything in is 0.4900000 number of dielectric boundary points 29191 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19318 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) : 0.6192920 object centre at (A) : -6.909500 -0.2560005 16.25350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1121163E-02 2.8254552E-02 midg,1,midg; midg,igrid,midg 1.2457275E-02 1.3227982E-03 1,midg,midg; igrid,midg,midg -1.4147945E-03 3.6427401E-02 gauss-seidel spectral radius is 0.9985628 estimated iterations to convergence 209 setup time was (sec) 0.7900000 now iterating at: 20:33:05 rms-change max change #iterations 4.016576 173.9654 at 10iterations 1.847663 61.95376 at 20iterations 0.8452122 27.50659 at 30iterations 0.3872935 12.86918 at 40iterations 0.1788981 5.874105 at 50iterations 8.1978768E-02 2.574314 at 60iterations 3.7694003E-02 1.308842 at 70iterations 1.7299935E-02 0.5598950 at 80iterations 7.9559581E-03 0.2499838 at 90iterations 3.6612561E-03 0.1288815 at 100iterations 1.6814421E-03 5.8280945E-02 at 110iterations 7.7138701E-04 2.6710510E-02 at 120iterations finished qdiffx linear iterations at : 20:33:12 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 7.7138701E-04 2.6710510E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 20:33:12 7.494u 0.233s 0:08.00 96.5% 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 Sat Oct 8 2011 at 20:33:12 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 2.786814 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): -31.33300 17.51400 ymin,ymax (A): -23.56500 23.05300 zmin,zma (A): -12.48900 44.99600 x,y,z range (A): 48.84700 46.61800 57.48500 scale (grids/A): 2.786814 object centre (A): -6.909500 -0.2560005 16.25350 number of atom coordinates read : 2605 total number of charged atoms : 2462 net assigned charge : 4.406006 assigned positive charge : 394.2350 centred at (gu) : 83.29258 86.17031 88.15437 assigned negative charge : -389.8296 centred at (gu) : 82.84861 86.44244 87.63453 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 162163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21554 grid for indexing accessible points = 1.400000 m= 79112 mr = 118086 m= 26142 mr = 64584 m= 5768 mr = 20849 m= 746 mr = 4198 m= 45 mr = 465 m= 0 mr = 17 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 10926 time to turn everything in is 1.230000 number of dielectric boundary points 65777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 19695 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) : 1.857876 object centre at (A) : -6.909500 -0.2560005 16.25350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1235893 0.3604361 midg,1,midg; midg,igrid,midg 0.1462449 -3.7211410E-03 1,midg,midg; igrid,midg,midg -2.1452334E-02 0.4727478 gauss-seidel spectral radius is 0.9992327 estimated iterations to convergence 285 setup time was (sec) 1.540000 now iterating at: 20:33:14 rms-change max change #iterations 9.456577 446.5524 at 10iterations 5.442339 119.9415 at 20iterations 3.103160 66.92358 at 30iterations 1.772217 39.75719 at 40iterations 1.009473 22.99568 at 50iterations 0.5749214 12.28135 at 60iterations 0.3283004 6.812393 at 70iterations 0.1860520 3.426502 at 80iterations 0.1059348 2.135435 at 90iterations 6.0297605E-02 1.111723 at 100iterations 3.4243725E-02 0.7025127 at 110iterations 1.9516269E-02 0.3964272 at 120iterations 1.1098323E-02 0.2013426 at 130iterations 6.2958449E-03 0.1188202 at 140iterations 3.5842517E-03 7.4144363E-02 at 150iterations 2.0409108E-03 3.7258148E-02 at 160iterations 1.1603343E-03 2.1923065E-02 at 170iterations 6.6001376E-04 1.3214111E-02 at 180iterations finished qdiffx linear iterations at : 20:33:24 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 6.6001376E-04 1.3214111E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 20:33:25 12.194u 0.247s 0:12.70 97.8% 0+0k 0+0io 0pf+0w