Mon Oct 10 14:02:36 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 Mon Oct 10 2011 at 14:02:36 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2139 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: 0.7199628 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): 13.66800 59.07500 ymin,ymax (A): 5.892000 48.88400 zmin,zma (A): -24.36100 25.08600 x,y,z range (A): 45.40700 42.99200 49.44700 scale (grids/A): 0.7199628 object centre (A): 36.37150 27.38800 0.3625002 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -5.999980 assigned positive charge : 320.7838 centred at (gu) : 89.35276 91.57542 91.07578 assigned negative charge : -326.7840 centred at (gu) : 89.49589 91.43646 90.89793 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7448 nv = 96 ne = 84 npr = 44659 no. pairs analyzed = 44659 no. exposed pairs = 2667 no. arc points = 18962 no. surface atoms = 899 nbur = 1240 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 4074 m= 1 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2800000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1588 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8156 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5792391E-07 6.0125089E-08 midg,1,midg; midg,igrid,midg -1.2360140E-07 3.1968728E-08 1,midg,midg; igrid,midg,midg 2.8854798E-08 -1.4991852E-07 gauss-seidel spectral radius is 0.9899514 estimated iterations to convergence 81 setup time was (sec) 0.6200000 now iterating at: 14:02:37 rms-change max change #iterations 0.2218178 29.14329 at 10iterations 2.8336676E-02 4.235954 at 20iterations 3.6077299E-03 0.5293722 at 30iterations 4.6022946E-04 6.0821533E-02 at 40iterations 5.9058082E-05 8.6469650E-03 at 50iterations finished qdiffx linear iterations at : 14:02:41 total time elapsed so far: 4.700000 # loops : 50 mean,max change (kT/e) : 5.9058082E-05 8.6469650E-03 energy calculations done at 4.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.910000 DelPhi exited at 14:02:42 4.909u 0.262s 0:05.62 91.8% 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 Mon Oct 10 2011 at 14:02:42 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2139 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: 2.159889 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): 13.66800 59.07500 ymin,ymax (A): 5.892000 48.88400 zmin,zma (A): -24.36100 25.08600 x,y,z range (A): 45.40700 42.99200 49.44700 scale (grids/A): 2.159889 object centre (A): 36.37150 27.38800 0.3625002 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -5.999980 assigned positive charge : 320.7838 centred at (gu) : 88.05805 94.72599 93.22739 assigned negative charge : -326.7840 centred at (gu) : 88.48775 94.30945 92.69395 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 78496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18962 grid for indexing accessible points = 1.400000 m= 29957 mr = 53742 m= 5873 mr = 22426 m= 579 mr = 3974 m= 17 mr = 298 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 795 time to turn everything in is 0.6300000 number of dielectric boundary points 34480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15922 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) : 0.7199628 object centre at (A) : 36.37150 27.38800 0.3625002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8958038E-02 -2.9057389E-02 midg,1,midg; midg,igrid,midg -3.6544651E-02 -2.8462209E-02 1,midg,midg; igrid,midg,midg 2.6576353E-02 -1.1190585E-02 gauss-seidel spectral radius is 0.9988745 estimated iterations to convergence 236 setup time was (sec) 0.9600000 now iterating at: 14:02:43 rms-change max change #iterations 4.863832 192.0367 at 10iterations 2.426104 80.32491 at 20iterations 1.218599 37.65184 at 30iterations 0.6094922 19.06763 at 40iterations 0.3060887 9.034985 at 50iterations 0.1534677 4.499341 at 60iterations 7.6880552E-02 2.310753 at 70iterations 3.8603533E-02 1.152009 at 80iterations 1.9409863E-02 0.5331821 at 90iterations 9.7483201E-03 0.2774963 at 100iterations 4.8915870E-03 0.1369820 at 110iterations 2.4471544E-03 7.2826385E-02 at 120iterations finished qdiffx linear iterations at : 14:02:50 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 2.4471544E-03 7.2826385E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.410000 DelPhi exited at 14:02:51 8.418u 0.230s 0:08.99 96.1% 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 Mon Oct 10 2011 at 14:02:51 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2139 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: 3.239833 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): 13.66800 59.07500 ymin,ymax (A): 5.892000 48.88400 zmin,zma (A): -24.36100 25.08600 x,y,z range (A): 45.40700 42.99200 49.44700 scale (grids/A): 3.239833 object centre (A): 36.37150 27.38800 0.3625002 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -5.999980 assigned positive charge : 320.7838 centred at (gu) : 87.08720 97.08889 94.84109 assigned negative charge : -326.7840 centred at (gu) : 87.73158 96.46413 94.04089 start vw surface at 0.1800000 fill in re-entrant regions at 0.9400000 boundary points on vw surface= 180839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18962 grid for indexing accessible points = 1.400000 m= 93188 mr = 129595 m= 37684 mr = 76779 m= 11259 mr = 30794 m= 2425 mr = 8779 m= 314 mr = 1833 m= 14 mr = 197 m= 0 mr = 1 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 2744 time to turn everything in is 2.000000 number of dielectric boundary points 77745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 15992 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) : 2.159889 object centre at (A) : 36.37150 27.38800 0.3625002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8042115 -0.3187113 midg,1,midg; midg,igrid,midg -0.2389858 -0.2625627 1,midg,midg; igrid,midg,midg 0.1511526 -6.5133169E-02 gauss-seidel spectral radius is 0.9993082 estimated iterations to convergence 300 setup time was (sec) 2.350000 now iterating at: 14:02:54 rms-change max change #iterations 10.71297 329.8577 at 10iterations 6.283141 131.8118 at 20iterations 3.692166 67.03963 at 30iterations 2.160898 52.15010 at 40iterations 1.264624 23.94740 at 50iterations 0.7419896 13.43928 at 60iterations 0.4338246 7.198720 at 70iterations 0.2534406 4.340678 at 80iterations 0.1481064 2.695778 at 90iterations 8.6461797E-02 1.358368 at 100iterations 5.0653633E-02 1.046436 at 110iterations 2.9635150E-02 0.5208969 at 120iterations 1.7361389E-02 0.2794228 at 130iterations 1.0121791E-02 0.1810871 at 140iterations 5.9209270E-03 0.1000501 at 150iterations 3.4626196E-03 5.3679466E-02 at 160iterations 2.0260401E-03 3.1594038E-02 at 170iterations 1.1853968E-03 2.0337820E-02 at 180iterations finished qdiffx linear iterations at : 14:03:05 total time elapsed so far: 13.79000 # loops : 180 mean,max change (kT/e) : 1.1853968E-03 2.0337820E-02 energy calculations done at 13.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.97000 DelPhi exited at 14:03:06 13.976u 0.247s 0:14.84 95.7% 0+0k 0+0io 0pf+0w