Sat Oct 8 14:53:49 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 Sat Oct 8 2011 at 14:53:49 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 0.6058544 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): 27.94400 86.70399 ymin,ymax (A): 11.61800 64.67000 zmin,zma (A): 70.61500 117.7130 x,y,z range (A): 58.75999 53.05200 47.09800 scale (grids/A): 0.6058544 object centre (A): 57.32400 38.14400 94.16400 number of atom coordinates read : 3036 total number of charged atoms : 2888 net assigned charge : -3.499991 assigned positive charge : 454.0375 centred at (gu) : 89.95374 90.06371 89.83057 assigned negative charge : -457.5382 centred at (gu) : 90.03171 90.15775 89.73824 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7125 nv = 96 ne = 84 npr = 64935 no. pairs analyzed = 64935 no. exposed pairs = 3373 no. arc points = 23297 no. surface atoms = 1156 nbur = 1880 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 4155 m= 2 mr = 23 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 0.3900000 number of dielectric boundary points 3302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2288 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9036 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8615313E-09 2.7976099E-09 midg,1,midg; midg,igrid,midg 2.9532561E-09 -6.7903283E-09 1,midg,midg; igrid,midg,midg 2.2102602E-09 -5.7876606E-09 gauss-seidel spectral radius is 0.9859226 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 14:53:50 rms-change max change #iterations 0.1288074 16.45641 at 10iterations 1.1314869E-02 1.491936 at 20iterations 1.0502110E-03 0.1600494 at 30iterations 1.0351194E-04 1.5298843E-02 at 40iterations 1.2649708E-05 1.7967224E-03 at 50iterations finished qdiffx linear iterations at : 14:53:53 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.2649708E-05 1.7967224E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 14:53:54 4.185u 0.254s 0:04.83 91.7% 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 14:53:54 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 1.817563 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): 27.94400 86.70399 ymin,ymax (A): 11.61800 64.67000 zmin,zma (A): 70.61500 117.7130 x,y,z range (A): 58.75999 53.05200 47.09800 scale (grids/A): 1.817563 object centre (A): 57.32400 38.14400 94.16400 number of atom coordinates read : 3036 total number of charged atoms : 2888 net assigned charge : -3.499991 assigned positive charge : 454.0375 centred at (gu) : 89.86067 90.19060 89.49096 assigned negative charge : -457.5382 centred at (gu) : 90.09466 90.47308 89.21478 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 79028 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23297 grid for indexing accessible points = 1.400000 m= 26526 mr = 57159 m= 3223 mr = 19506 m= 126 mr = 1760 m= 0 mr = 39 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 30439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22630 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) : 0.6058544 object centre at (A) : 57.32400 38.14400 94.16400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7363272E-03 1.0367037E-02 midg,1,midg; midg,igrid,midg -1.5078590E-02 -3.8103901E-02 1,midg,midg; igrid,midg,midg 1.0487733E-02 -2.6141193E-02 gauss-seidel spectral radius is 0.9985370 estimated iterations to convergence 207 setup time was (sec) 1.000000 now iterating at: 14:53:55 rms-change max change #iterations 4.265786 171.6596 at 10iterations 1.939064 66.71635 at 20iterations 0.8849574 29.35747 at 30iterations 0.4047856 12.26013 at 40iterations 0.1857972 6.262494 at 50iterations 8.4740512E-02 2.529129 at 60iterations 3.8764112E-02 1.210852 at 70iterations 1.7718885E-02 0.5977821 at 80iterations 8.1230905E-03 0.2495480 at 90iterations 3.7181822E-03 0.1173636 at 100iterations 1.6969187E-03 5.4489136E-02 at 110iterations 7.8057626E-04 2.4929047E-02 at 120iterations finished qdiffx linear iterations at : 14:54:04 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 7.8057626E-04 2.4929047E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 14:54:04 9.597u 0.304s 0:10.18 97.1% 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 Sat Oct 8 2011 at 14:54:04 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 2.726345 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): 27.94400 86.70399 ymin,ymax (A): 11.61800 64.67000 zmin,zma (A): 70.61500 117.7130 x,y,z range (A): 58.75999 53.05200 47.09800 scale (grids/A): 2.726345 object centre (A): 57.32400 38.14400 94.16400 number of atom coordinates read : 3036 total number of charged atoms : 2888 net assigned charge : -3.499991 assigned positive charge : 454.0375 centred at (gu) : 89.79080 90.28580 89.23627 assigned negative charge : -457.5382 centred at (gu) : 90.14192 90.70963 88.82207 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 183675 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23297 grid for indexing accessible points = 1.400000 m= 89273 mr = 138553 m= 28357 mr = 73683 m= 5261 mr = 22336 m= 492 mr = 3653 m= 33 mr = 289 m= 0 mr = 9 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 68568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 23102 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) : 1.817563 object centre at (A) : 57.32400 38.14400 94.16400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0438377E-02 0.1061174 midg,1,midg; midg,igrid,midg -0.1980755 -0.3665970 1,midg,midg; igrid,midg,midg 0.1954215 -0.2053645 gauss-seidel spectral radius is 0.9992296 estimated iterations to convergence 284 setup time was (sec) 2.060000 now iterating at: 14:54:07 rms-change max change #iterations 10.08709 327.0984 at 10iterations 5.821549 134.0088 at 20iterations 3.333257 78.30353 at 30iterations 1.910774 39.88386 at 40iterations 1.089810 22.02695 at 50iterations 0.6204082 13.29151 at 60iterations 0.3540588 6.441464 at 70iterations 0.2019460 3.701890 at 80iterations 0.1148891 2.092692 at 90iterations 6.5478377E-02 1.182123 at 100iterations 3.7261527E-02 0.6699274 at 110iterations 2.1199178E-02 0.3884952 at 120iterations 1.2057234E-02 0.2076864 at 130iterations 6.8581081E-03 0.1317291 at 140iterations 3.9110547E-03 6.9747925E-02 at 150iterations 2.2361523E-03 4.0503383E-02 at 160iterations 1.2817177E-03 2.1961212E-02 at 170iterations 7.3741149E-04 1.4041543E-02 at 180iterations finished qdiffx linear iterations at : 14:54:21 total time elapsed so far: 15.95000 # loops : 180 mean,max change (kT/e) : 7.3741149E-04 1.4041543E-02 energy calculations done at 15.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.12000 DelPhi exited at 14:54:21 16.123u 0.338s 0:16.79 97.9% 0+0k 0+0io 0pf+0w