Mon Oct 10 09:14:34 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 09:14:34 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6376044 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): -5.839000 35.33100 ymin,ymax (A): -3.713000 49.00500 zmin,zma (A): -24.53700 31.29700 x,y,z range (A): 41.17000 52.71800 55.83400 scale (grids/A): 0.6376044 object centre (A): 14.74600 22.64600 3.380001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 90.80302 92.50884 90.22551 assigned negative charge : -288.8263 centred at (gu) : 90.93567 92.62493 90.16980 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 39388 no. pairs analyzed = 39388 no. exposed pairs = 2524 no. arc points = 17977 no. surface atoms = 859 nbur = 1105 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3123 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1757 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6454 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2371701E-11 9.3100185E-09 midg,1,midg; midg,igrid,midg 8.0155855E-09 -9.0733945E-09 1,midg,midg; igrid,midg,midg 1.2579904E-08 -7.7300140E-09 gauss-seidel spectral radius is 0.9872054 estimated iterations to convergence 72 setup time was (sec) 0.3400000 now iterating at: 09:14:35 rms-change max change #iterations 0.1287213 21.17807 at 10iterations 1.2541362E-02 2.441826 at 20iterations 1.2352226E-03 0.2147136 at 30iterations 1.1925713E-04 2.2459030E-02 at 40iterations 1.1454539E-05 1.8892288E-03 at 50iterations finished qdiffx linear iterations at : 09:14:38 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1454539E-05 1.8892288E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 09:14:38 3.350u 0.179s 0:03.86 91.1% 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 09:14:38 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.912813 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): -5.839000 35.33100 ymin,ymax (A): -3.713000 49.00500 zmin,zma (A): -24.53700 31.29700 x,y,z range (A): 41.17000 52.71800 55.83400 scale (grids/A): 1.912813 object centre (A): 14.74600 22.64600 3.380001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 92.40903 97.52638 90.67644 assigned negative charge : -288.8263 centred at (gu) : 92.80729 97.87495 90.50949 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 59820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17977 grid for indexing accessible points = 1.400000 m= 23269 mr = 40940 m= 4138 mr = 17932 m= 255 mr = 3008 m= 1 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1607 time to turn everything in is 0.3000000 number of dielectric boundary points 25489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14418 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) : 0.6376044 object centre at (A) : 14.74600 22.64600 3.380001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5361131E-02 1.2438556E-02 midg,1,midg; midg,igrid,midg 2.8953061E-02 -6.8215309E-03 1,midg,midg; igrid,midg,midg 7.3490487E-03 -5.1578567E-03 gauss-seidel spectral radius is 0.9985741 estimated iterations to convergence 210 setup time was (sec) 0.5200000 now iterating at: 09:14:39 rms-change max change #iterations 3.654675 158.8952 at 10iterations 1.681358 60.26169 at 20iterations 0.7748566 29.10786 at 30iterations 0.3575403 13.29368 at 40iterations 0.1639666 6.281349 at 50iterations 7.5613759E-02 2.476646 at 60iterations 3.4752764E-02 1.172586 at 70iterations 1.5956571E-02 0.5369072 at 80iterations 7.3607950E-03 0.2452674 at 90iterations 3.3970356E-03 0.1221170 at 100iterations 1.5653222E-03 5.7037458E-02 at 110iterations 7.1784877E-04 2.3918152E-02 at 120iterations finished qdiffx linear iterations at : 09:14:46 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 7.1784877E-04 2.3918152E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 09:14:46 7.694u 0.201s 0:08.27 95.4% 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 09:14:47 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.869220 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): -5.839000 35.33100 ymin,ymax (A): -3.713000 49.00500 zmin,zma (A): -24.53700 31.29700 x,y,z range (A): 41.17000 52.71800 55.83400 scale (grids/A): 2.869220 object centre (A): 14.74600 22.64600 3.380001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 93.61347 101.2896 91.01467 assigned negative charge : -288.8263 centred at (gu) : 94.21095 101.8125 90.76430 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 137934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17977 grid for indexing accessible points = 1.400000 m= 72773 mr = 98783 m= 29233 mr = 60646 m= 7780 mr = 24680 m= 1149 mr = 6413 m= 72 mr = 872 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 5520 time to turn everything in is 0.7900000 number of dielectric boundary points 57511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14656 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) : 1.912813 object centre at (A) : 14.74600 22.64600 3.380001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.096995 -7.8838384E-03 midg,1,midg; midg,igrid,midg 0.2772963 -0.1007436 1,midg,midg; igrid,midg,midg 4.1054569E-02 -2.9301094E-02 gauss-seidel spectral radius is 0.9992313 estimated iterations to convergence 285 setup time was (sec) 1.010000 now iterating at: 09:14:48 rms-change max change #iterations 8.618226 442.9936 at 10iterations 4.950968 136.8632 at 20iterations 2.816049 64.03637 at 30iterations 1.604907 34.84643 at 40iterations 0.9134105 22.69492 at 50iterations 0.5179223 11.01767 at 60iterations 0.2940981 6.200670 at 70iterations 0.1675471 3.738020 at 80iterations 9.4663337E-02 1.992558 at 90iterations 5.3790692E-02 1.032085 at 100iterations 3.0507021E-02 0.6113820 at 110iterations 1.7328015E-02 0.3772026 at 120iterations 9.7995084E-03 0.2052479 at 130iterations 5.5587995E-03 0.1189880 at 140iterations 3.1482491E-03 6.3497543E-02 at 150iterations 1.7954290E-03 3.6663055E-02 at 160iterations 1.0159450E-03 1.9929886E-02 at 170iterations 5.7743187E-04 1.3173580E-02 at 180iterations finished qdiffx linear iterations at : 09:14:59 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 5.7743187E-04 1.3173580E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 09:14:59 12.015u 0.196s 0:12.48 97.7% 0+0k 0+0io 0pf+0w