Mon Oct 10 18:48:05 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 Mon Oct 10 2011 at 18:48:05 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2183 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: 0.6171662 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): -9.595000 48.08800 ymin,ymax (A): 63.44100 117.8920 zmin,zma (A): 47.13900 87.92900 x,y,z range (A): 57.68300 54.45100 40.79000 scale (grids/A): 0.6171662 object centre (A): 19.24650 90.66650 67.53400 number of atom coordinates read : 2183 total number of charged atoms : 2046 net assigned charge : 5.8710575E-06 assigned positive charge : 325.8822 centred at (gu) : 88.34660 90.67181 90.48492 assigned negative charge : -325.8827 centred at (gu) : 88.44513 90.74061 90.58254 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5684 nv = 96 ne = 84 npr = 43829 no. pairs analyzed = 43829 no. exposed pairs = 2846 no. arc points = 19754 no. surface atoms = 963 nbur = 1220 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 314 mr = 3066 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2005 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6887 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4050634E-09 -5.6792118E-09 midg,1,midg; midg,igrid,midg 2.9782403E-09 -4.1736121E-09 1,midg,midg; igrid,midg,midg 7.2244406E-09 -3.5503946E-09 gauss-seidel spectral radius is 0.9863730 estimated iterations to convergence 70 setup time was (sec) 0.4800000 now iterating at: 18:48:05 rms-change max change #iterations 0.1139729 16.39287 at 10iterations 1.0441457E-02 1.626221 at 20iterations 9.8577689E-04 0.1530609 at 30iterations 1.1971071E-04 2.0347595E-02 at 40iterations 2.2690236E-05 4.3830872E-03 at 50iterations finished qdiffx linear iterations at : 18:48:08 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 2.2690236E-05 4.3830872E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 18:48:08 3.143u 0.170s 0:03.61 91.6% 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 Mon Oct 10 2011 at 18:48:08 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2183 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: 1.851499 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): -9.595000 48.08800 ymin,ymax (A): 63.44100 117.8920 zmin,zma (A): 47.13900 87.92900 x,y,z range (A): 57.68300 54.45100 40.79000 scale (grids/A): 1.851499 object centre (A): 19.24650 90.66650 67.53400 number of atom coordinates read : 2183 total number of charged atoms : 2046 net assigned charge : 5.8710575E-06 assigned positive charge : 325.8822 centred at (gu) : 85.03938 92.01504 91.45435 assigned negative charge : -325.8827 centred at (gu) : 85.33511 92.22150 91.74744 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19754 grid for indexing accessible points = 1.400000 m= 22488 mr = 42021 m= 3362 mr = 16451 m= 161 mr = 1957 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 26796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 16047 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) : 0.6171662 object centre at (A) : 19.24650 90.66650 67.53400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2728287E-03 -7.8453403E-04 midg,1,midg; midg,igrid,midg 1.8006179E-02 -1.4717209E-02 1,midg,midg; igrid,midg,midg -2.9542784E-03 -1.0607264E-02 gauss-seidel spectral radius is 0.9985183 estimated iterations to convergence 206 setup time was (sec) 0.7200000 now iterating at: 18:48:09 rms-change max change #iterations 3.636513 164.6928 at 10iterations 1.639345 65.61626 at 20iterations 0.7448583 28.47465 at 30iterations 0.3367127 12.46713 at 40iterations 0.1528050 5.528403 at 50iterations 6.9318689E-02 2.516181 at 60iterations 3.1512029E-02 1.098953 at 70iterations 1.4255511E-02 0.5052009 at 80iterations 6.4807949E-03 0.2172098 at 90iterations 2.9511901E-03 0.1066284 at 100iterations 1.3500772E-03 5.3962708E-02 at 110iterations 6.1941356E-04 2.2914886E-02 at 120iterations finished qdiffx linear iterations at : 18:48:15 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 6.1941356E-04 2.2914886E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 18:48:16 7.012u 0.205s 0:07.67 94.0% 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 18:48:16 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2183 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: 2.777248 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): -9.595000 48.08800 ymin,ymax (A): 63.44100 117.8920 zmin,zma (A): 47.13900 87.92900 x,y,z range (A): 57.68300 54.45100 40.79000 scale (grids/A): 2.777248 object centre (A): 19.24650 90.66650 67.53400 number of atom coordinates read : 2183 total number of charged atoms : 2046 net assigned charge : 5.8710575E-06 assigned positive charge : 325.8822 centred at (gu) : 82.55904 93.02244 92.18137 assigned negative charge : -325.8827 centred at (gu) : 83.00264 93.33222 92.62107 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 141538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19754 grid for indexing accessible points = 1.400000 m= 72239 mr = 102091 m= 26257 mr = 58698 m= 5898 mr = 20785 m= 658 mr = 4182 m= 21 mr = 332 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 60523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 16365 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) : 1.851499 object centre at (A) : 19.24650 90.66650 67.53400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8604182E-02 2.1240704E-02 midg,1,midg; midg,igrid,midg 0.3633892 -0.1933093 1,midg,midg; igrid,midg,midg -9.3940146E-02 4.0979464E-02 gauss-seidel spectral radius is 0.9992179 estimated iterations to convergence 282 setup time was (sec) 1.350000 now iterating at: 18:48:18 rms-change max change #iterations 8.754118 322.9199 at 10iterations 5.094594 124.9365 at 20iterations 2.927757 81.62955 at 30iterations 1.678311 39.37319 at 40iterations 0.9571739 19.88621 at 50iterations 0.5459656 12.53504 at 60iterations 0.3100123 6.405735 at 70iterations 0.1758081 3.790343 at 80iterations 0.1000354 2.051105 at 90iterations 5.6759108E-02 1.074978 at 100iterations 3.2130063E-02 0.7318517 at 110iterations 1.8242365E-02 0.3358574 at 120iterations 1.0329021E-02 0.2170515 at 130iterations 5.8581866E-03 0.1222343 at 140iterations 3.3263508E-03 6.8738937E-02 at 150iterations 1.8858719E-03 3.6964417E-02 at 160iterations 1.0804785E-03 2.2842407E-02 at 170iterations 6.2289106E-04 1.3130188E-02 at 180iterations finished qdiffx linear iterations at : 18:48:28 total time elapsed so far: 11.21000 # loops : 180 mean,max change (kT/e) : 6.2289106E-04 1.3130188E-02 energy calculations done at 11.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.38000 DelPhi exited at 18:48:28 11.383u 0.184s 0:12.12 95.3% 0+0k 0+0io 0pf+0w