Sat Oct 8 18:40:52 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 18:40:53 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2601 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 501 has a net charge of 1.4000 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: 0.6322482 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): -31.89000 17.56900 ymin,ymax (A): -23.79700 22.34400 zmin,zma (A): -11.97500 44.33200 x,y,z range (A): 49.45900 46.14100 56.30700 scale (grids/A): 0.6322482 object centre (A): -7.160501 -0.7264996 16.17850 number of atom coordinates read : 2601 total number of charged atoms : 2482 net assigned charge : 4.500006 assigned positive charge : 395.4250 centred at (gu) : 88.46970 89.47191 89.89555 assigned negative charge : -390.9255 centred at (gu) : 88.36986 89.51016 89.78071 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6886 nv = 96 ne = 84 npr = 53648 no. pairs analyzed = 53648 no. exposed pairs = 2999 no. arc points = 21537 no. surface atoms = 1017 nbur = 1584 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3913 m= 0 mr = 54 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 121 time to turn everything in is 0.3000000 number of dielectric boundary points 3270 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2101 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8356 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7600027E-09 1.5751446E-08 midg,1,midg; midg,igrid,midg 1.0064467E-08 1.5853604E-09 1,midg,midg; igrid,midg,midg -5.9986585E-09 1.0606477E-08 gauss-seidel spectral radius is 0.9870383 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 18:40:53 rms-change max change #iterations 0.1396574 23.25958 at 10iterations 1.3412680E-02 2.010674 at 20iterations 1.2993418E-03 0.1761594 at 30iterations 1.2324924E-04 2.7141571E-02 at 40iterations 1.2050997E-05 1.7166138E-03 at 50iterations finished qdiffx linear iterations at : 18:40:56 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.2050997E-05 1.7166138E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 18:40:56 3.081u 0.137s 0:03.49 91.9% 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 18:40:56 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2601 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 501 has a net charge of 1.4000 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: 1.896745 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): -31.89000 17.56900 ymin,ymax (A): -23.79700 22.34400 zmin,zma (A): -11.97500 44.33200 x,y,z range (A): 49.45900 46.14100 56.30700 scale (grids/A): 1.896745 object centre (A): -7.160501 -0.7264996 16.17850 number of atom coordinates read : 2601 total number of charged atoms : 2482 net assigned charge : 4.500006 assigned positive charge : 395.4250 centred at (gu) : 85.40877 88.41525 89.68629 assigned negative charge : -390.9255 centred at (gu) : 85.10943 88.53004 89.34181 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21537 grid for indexing accessible points = 1.400000 m= 27150 mr = 52456 m= 4003 mr = 20496 m= 239 mr = 2500 m= 2 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 5399 time to turn everything in is 0.5300000 number of dielectric boundary points 30436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19556 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) : 0.6322482 object centre at (A) : -7.160501 -0.7264996 16.17850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2354243E-02 3.4466065E-02 midg,1,midg; midg,igrid,midg 1.3744914E-02 1.7360469E-03 1,midg,midg; igrid,midg,midg -1.6909530E-03 4.0011272E-02 gauss-seidel spectral radius is 0.9986200 estimated iterations to convergence 213 setup time was (sec) 0.8200000 now iterating at: 18:40:57 rms-change max change #iterations 4.219173 170.9937 at 10iterations 1.964385 72.63954 at 20iterations 0.9164398 34.57842 at 30iterations 0.4259942 12.86819 at 40iterations 0.1999714 7.086052 at 50iterations 9.3132287E-02 3.007956 at 60iterations 4.3430809E-02 1.350807 at 70iterations 2.0308696E-02 0.6568344 at 80iterations 9.4317356E-03 0.3198667 at 90iterations 4.4140923E-03 0.1379051 at 100iterations 2.0622355E-03 6.1863899E-02 at 110iterations 9.6190738E-04 2.9508829E-02 at 120iterations finished qdiffx linear iterations at : 18:41:04 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 9.6190738E-04 2.9508829E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 18:41:05 8.127u 0.288s 0:08.75 96.0% 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 Sat Oct 8 2011 at 18:41:05 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2601 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 501 has a net charge of 1.4000 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: 2.845117 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): -31.89000 17.56900 ymin,ymax (A): -23.79700 22.34400 zmin,zma (A): -11.97500 44.33200 x,y,z range (A): 49.45900 46.14100 56.30700 scale (grids/A): 2.845117 object centre (A): -7.160501 -0.7264996 16.17850 number of atom coordinates read : 2601 total number of charged atoms : 2482 net assigned charge : 4.500006 assigned positive charge : 395.4250 centred at (gu) : 83.11312 87.62283 89.52927 assigned negative charge : -390.9255 centred at (gu) : 82.66407 87.79506 89.01264 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 172352 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21537 grid for indexing accessible points = 1.400000 m= 88780 mr = 126746 m= 31246 mr = 73692 m= 7084 mr = 25407 m= 1003 mr = 5377 m= 65 mr = 736 m= 0 mr = 28 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 17986 time to turn everything in is 1.350000 number of dielectric boundary points 68544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 19854 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) : 1.896745 object centre at (A) : -7.160501 -0.7264996 16.17850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1529789 0.3926737 midg,1,midg; midg,igrid,midg 0.1691632 -4.6338215E-03 1,midg,midg; igrid,midg,midg 2.0362996E-02 0.4849534 gauss-seidel spectral radius is 0.9992490 estimated iterations to convergence 288 setup time was (sec) 1.690000 now iterating at: 18:41:07 rms-change max change #iterations 9.851503 376.0491 at 10iterations 5.697781 137.1389 at 20iterations 3.262232 93.29324 at 30iterations 1.874565 37.03126 at 40iterations 1.074211 20.17938 at 50iterations 0.6162912 13.44122 at 60iterations 0.3525157 6.580572 at 70iterations 0.2017757 3.816540 at 80iterations 0.1155073 2.482306 at 90iterations 6.6091962E-02 1.347052 at 100iterations 3.7849821E-02 0.6899147 at 110iterations 2.1646680E-02 0.4358444 at 120iterations 1.2397617E-02 0.2210598 at 130iterations 7.0712646E-03 0.1283493 at 140iterations 4.0540802E-03 7.1382999E-02 at 150iterations 2.3148132E-03 4.3464661E-02 at 160iterations 1.3226520E-03 2.5690079E-02 at 170iterations 7.5568201E-04 1.3248444E-02 at 180iterations finished qdiffx linear iterations at : 18:41:19 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 7.5568201E-04 1.3248444E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.69000 DelPhi exited at 18:41:19 13.693u 0.281s 0:14.25 98.0% 0+0k 0+0io 0pf+0w