Sat Oct 8 16:56:07 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 16:56:07 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4503 !!! WARNING: GLM 204 has a net charge of -0.0940 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: 0.5608065 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): 21.05400 78.94900 ymin,ymax (A): 118.0070 181.4870 zmin,zma (A): -1.677000 52.98200 x,y,z range (A): 57.89500 63.48000 54.65900 scale (grids/A): 0.5608065 object centre (A): 50.00150 149.7470 25.65250 number of atom coordinates read : 4503 total number of charged atoms : 4364 net assigned charge : 1.406044 assigned positive charge : 692.5894 centred at (gu) : 90.76786 89.71368 88.72599 assigned negative charge : -691.1868 centred at (gu) : 90.79760 89.64626 88.81892 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9270 nv = 96 ne = 84 npr = 90252 no. pairs analyzed = 90252 no. exposed pairs = 5611 no. arc points = 38584 no. surface atoms = 1867 nbur = 2636 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 389 mr = 5017 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3918 ## 446 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 12097 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4169615E-09 -1.1147905E-09 midg,1,midg; midg,igrid,midg -1.1414780E-09 1.2334691E-09 1,midg,midg; igrid,midg,midg 5.5136001E-10 -4.7134230E-10 gauss-seidel spectral radius is 0.9837153 estimated iterations to convergence 64 setup time was (sec) 0.4700000 now iterating at: 16:56:08 rms-change max change #iterations 0.1069042 14.83186 at 10iterations 8.4506515E-03 1.128422 at 20iterations 1.5921295E-03 0.2580948 at 30iterations 6.8395387E-04 0.1173210 at 40iterations 3.1491130E-04 5.4256439E-02 at 50iterations finished qdiffx linear iterations at : 16:56:11 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.1491130E-04 5.4256439E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 16:56:11 3.462u 0.185s 0:03.93 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 16:56:11 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4503 !!! WARNING: GLM 204 has a net charge of -0.0940 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: 1.682420 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): 21.05400 78.94900 ymin,ymax (A): 118.0070 181.4870 zmin,zma (A): -1.677000 52.98200 x,y,z range (A): 57.89500 63.48000 54.65900 scale (grids/A): 1.682420 object centre (A): 50.00150 149.7470 25.65250 number of atom coordinates read : 4503 total number of charged atoms : 4364 net assigned charge : 1.406044 assigned positive charge : 692.5894 centred at (gu) : 92.30241 89.13988 86.17690 assigned negative charge : -691.1868 centred at (gu) : 92.39247 88.93843 86.45640 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 103453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38584 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33957 mr = 72767 m= 4143 mr = 23524 m= 149 mr = 2182 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 768 time to turn everything in is 0.4900000 number of dielectric boundary points 43202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 418 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 33695 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) : 0.5608065 object centre at (A) : 50.00150 149.7470 25.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6928982E-03 -5.4745586E-03 midg,1,midg; midg,igrid,midg 1.8977882E-02 4.8311710E-02 1,midg,midg; igrid,midg,midg -1.8509319E-02 -2.1518620E-02 gauss-seidel spectral radius is 0.9984491 estimated iterations to convergence 201 setup time was (sec) 0.7200000 now iterating at: 16:56:12 rms-change max change #iterations 4.572684 181.3902 at 10iterations 2.026634 64.06756 at 20iterations 0.9065038 26.80455 at 30iterations 0.4016143 11.73230 at 40iterations 0.1800710 5.607378 at 50iterations 8.0454826E-02 2.700375 at 60iterations 3.6091857E-02 1.116352 at 70iterations 1.6198963E-02 0.4613609 at 80iterations 7.4486402E-03 0.2131634 at 90iterations 3.5856050E-03 0.1106033 at 100iterations 1.8877534E-03 6.2023163E-02 at 110iterations 1.1193677E-03 4.1625977E-02 at 120iterations finished qdiffx linear iterations at : 16:56:19 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 1.1193677E-03 4.1625977E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 16:56:20 8.038u 0.184s 0:08.49 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 Sat Oct 8 2011 at 16:56:20 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4503 !!! WARNING: GLM 204 has a net charge of -0.0940 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: 2.523629 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): 21.05400 78.94900 ymin,ymax (A): 118.0070 181.4870 zmin,zma (A): -1.677000 52.98200 x,y,z range (A): 57.89500 63.48000 54.65900 scale (grids/A): 2.523629 object centre (A): 50.00150 149.7470 25.65250 number of atom coordinates read : 4503 total number of charged atoms : 4364 net assigned charge : 1.406044 assigned positive charge : 692.5894 centred at (gu) : 93.45335 88.70928 84.26512 assigned negative charge : -691.1868 centred at (gu) : 93.58875 88.40759 84.68455 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 240340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38584 grid for indexing accessible points = 1.400000 m= 115973 mr = 177713 m= 35379 mr = 92388 m= 6867 mr = 26673 m= 673 mr = 4683 m= 14 mr = 344 m= 0 mr = 2 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 2732 time to turn everything in is 1.220000 number of dielectric boundary points 97443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 34888 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) : 1.682420 object centre at (A) : 50.00150 149.7470 25.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1251629E-02 -7.7714346E-02 midg,1,midg; midg,igrid,midg 0.3731022 0.8763902 1,midg,midg; igrid,midg,midg -0.2737718 -0.3345328 gauss-seidel spectral radius is 0.9992518 estimated iterations to convergence 289 setup time was (sec) 1.470000 now iterating at: 16:56:21 rms-change max change #iterations 11.55293 391.5459 at 10iterations 6.794605 201.7317 at 20iterations 3.977122 79.81179 at 30iterations 2.314429 49.08350 at 40iterations 1.343754 24.91834 at 50iterations 0.7781401 13.46959 at 60iterations 0.4494864 8.140738 at 70iterations 0.2591494 4.301046 at 80iterations 0.1494398 2.442215 at 90iterations 8.6006217E-02 1.431531 at 100iterations 4.9506977E-02 0.8317563 at 110iterations 2.8529478E-02 0.4744034 at 120iterations 1.6417712E-02 0.2817417 at 130iterations 9.5268097E-03 0.1555824 at 140iterations 5.5677481E-03 0.1088524 at 150iterations 3.3149924E-03 6.1508179E-02 at 160iterations 2.0414921E-03 4.1292191E-02 at 170iterations 1.3176650E-03 2.7465820E-02 at 180iterations finished qdiffx linear iterations at : 16:56:33 total time elapsed so far: 13.30000 # loops : 180 mean,max change (kT/e) : 1.3176650E-03 2.7465820E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 16:56:34 13.435u 0.207s 0:13.92 97.9% 0+0k 0+0io 0pf+0w