Tue Nov 22 14:12:00 PST 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 Nov 22 2011 at 14:12:02 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 = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6138566 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): -35.40300 9.708000 ymin,ymax (A): 0.8890001 41.82100 zmin,zma (A): -1.642000 56.35200 x,y,z range (A): 45.11100 40.93200 57.99400 scale (grids/A): 0.6138566 object centre (A): -12.84750 21.35500 27.35500 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000007 assigned positive charge : 287.8740 centred at (gu) : 90.57865 89.53207 90.34837 assigned negative charge : -282.8743 centred at (gu) : 90.54342 89.59474 90.34655 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4943 nv = 96 ne = 84 npr = 40814 no. pairs analyzed = 40814 no. exposed pairs = 2485 no. arc points = 17174 no. surface atoms = 840 nbur = 1128 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 225 mr = 2703 m= 0 mr = 17 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6003 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0016116E-09 3.6450631E-09 midg,1,midg; midg,igrid,midg 6.4594614E-09 6.9423045E-10 1,midg,midg; igrid,midg,midg 1.6662937E-09 5.3668767E-09 gauss-seidel spectral radius is 0.9862040 estimated iterations to convergence 70 setup time was (sec) 0.4600000 now iterating at: 14:12:04 rms-change max change #iterations 0.1017978 17.34121 at 10iterations 9.0049487E-03 1.478335 at 20iterations 8.0670521E-04 0.1368217 at 30iterations 7.1573952E-05 1.2822151E-02 at 40iterations 6.4191236E-06 1.0547638E-03 at 50iterations finished qdiffx linear iterations at : 14:12:11 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 6.4191236E-06 1.0547638E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 14:12:13 3.129u 0.145s 0:10.78 30.2% 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 Nov 22 2011 at 14:12:18 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 = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.841570 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): -35.40300 9.708000 ymin,ymax (A): 0.8890001 41.82100 zmin,zma (A): -1.642000 56.35200 x,y,z range (A): 45.11100 40.93200 57.99400 scale (grids/A): 1.841570 object centre (A): -12.84750 21.35500 27.35500 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000007 assigned positive charge : 287.8740 centred at (gu) : 91.73593 88.59610 91.04516 assigned negative charge : -282.8743 centred at (gu) : 91.63067 88.78455 91.03977 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 53346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17174 grid for indexing accessible points = 1.400000 m= 19275 mr = 36521 m= 2708 mr = 14266 m= 148 mr = 1664 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 22956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 14389 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) : 0.6138566 object centre at (A) : -12.84750 21.35500 27.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8396623E-02 3.0283581E-02 midg,1,midg; midg,igrid,midg 5.8934628E-03 9.5125852E-04 1,midg,midg; igrid,midg,midg 3.0947898E-03 -1.4206598E-03 gauss-seidel spectral radius is 0.9984638 estimated iterations to convergence 202 setup time was (sec) 0.6400000 now iterating at: 14:12:23 rms-change max change #iterations 3.284055 178.1118 at 10iterations 1.472216 58.49802 at 20iterations 0.6568537 24.97222 at 30iterations 0.2939045 10.54898 at 40iterations 0.1307937 4.441473 at 50iterations 5.8539066E-02 2.134682 at 60iterations 2.6192792E-02 0.9132662 at 70iterations 1.1660283E-02 0.4454346 at 80iterations 5.2461107E-03 0.1978378 at 90iterations 2.3388588E-03 9.1779709E-02 at 100iterations 1.0425544E-03 3.9025009E-02 at 110iterations 4.6959790E-04 1.9484699E-02 at 120iterations finished qdiffx linear iterations at : 14:12:41 total time elapsed so far: 6.550000 # loops : 120 mean,max change (kT/e) : 4.6959790E-04 1.9484699E-02 energy calculations done at 6.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.720000 DelPhi exited at 14:12:44 6.726u 0.150s 0:26.31 26.1% 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 Tue Nov 22 2011 at 14:12:46 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 = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.762355 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): -35.40300 9.708000 ymin,ymax (A): 0.8890001 41.82100 zmin,zma (A): -1.642000 56.35200 x,y,z range (A): 45.11100 40.93200 57.99400 scale (grids/A): 2.762355 object centre (A): -12.84750 21.35500 27.35500 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000007 assigned positive charge : 287.8740 centred at (gu) : 92.60378 87.89407 91.56770 assigned negative charge : -282.8743 centred at (gu) : 92.44591 88.17684 91.55961 start vw surface at 0.1200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 123089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17174 grid for indexing accessible points = 1.400000 m= 62375 mr = 88321 m= 22212 mr = 51110 m= 4851 mr = 17972 m= 625 mr = 3600 m= 42 mr = 436 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 51735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 14685 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) : 1.841570 object centre at (A) : -12.84750 21.35500 27.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9265455E-02 0.2527667 midg,1,midg; midg,igrid,midg 2.5292387E-02 2.8425369E-03 1,midg,midg; igrid,midg,midg 5.3599980E-03 -6.1164439E-02 gauss-seidel spectral radius is 0.9991937 estimated iterations to convergence 278 setup time was (sec) 1.260000 now iterating at: 14:12:52 rms-change max change #iterations 7.897757 296.3439 at 10iterations 4.524295 109.2413 at 20iterations 2.563272 60.36697 at 30iterations 1.442256 32.57764 at 40iterations 0.8119549 17.53685 at 50iterations 0.4572802 9.948292 at 60iterations 0.2559629 5.419420 at 70iterations 0.1434742 3.258703 at 80iterations 8.0466665E-02 1.752257 at 90iterations 4.5042839E-02 1.010880 at 100iterations 2.5249628E-02 0.5498838 at 110iterations 1.4182225E-02 0.2907076 at 120iterations 7.9224259E-03 0.1746273 at 130iterations 4.4334102E-03 8.7329388E-02 at 140iterations 2.4775341E-03 5.3947449E-02 at 150iterations 1.3882183E-03 3.0582428E-02 at 160iterations 7.7753881E-04 1.6429901E-02 at 170iterations 4.3486393E-04 9.2771053E-03 at 180iterations finished qdiffx linear iterations at : 14:13:23 total time elapsed so far: 11.29000 # loops : 180 mean,max change (kT/e) : 4.3486393E-04 9.2771053E-03 energy calculations done at 11.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 14:13:24 11.464u 0.186s 0:39.25 29.6% 0+0k 0+0io 0pf+0w