Tue Oct 11 03:25:11 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 Tue Oct 11 2011 at 03:25:11 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 = 2963 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: 0.5602593 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): -28.85500 24.34300 ymin,ymax (A): -67.82401 -8.929000 zmin,zma (A): -25.21800 38.32400 x,y,z range (A): 53.19800 58.89500 63.54200 scale (grids/A): 0.5602593 object centre (A): -2.256000 -38.37650 6.553000 number of atom coordinates read : 2963 total number of charged atoms : 2808 net assigned charge : -7.499990 assigned positive charge : 438.9932 centred at (gu) : 89.41113 91.81750 85.89729 assigned negative charge : -446.4945 centred at (gu) : 89.42480 91.83373 85.83657 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6252 nv = 96 ne = 84 npr = 57430 no. pairs analyzed = 57430 no. exposed pairs = 4194 no. arc points = 29778 no. surface atoms = 1388 nbur = 1575 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 265 mr = 2999 m= 0 mr = 18 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2922 ## 384 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7957 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8870058E-09 -4.8520254E-11 midg,1,midg; midg,igrid,midg -3.7999651E-10 -1.4327290E-09 1,midg,midg; igrid,midg,midg -6.9017042E-10 -7.8453427E-10 gauss-seidel spectral radius is 0.9835764 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 03:25:12 rms-change max change #iterations 8.1621900E-02 13.30745 at 10iterations 5.7848911E-03 1.013127 at 20iterations 4.0977265E-04 6.3095093E-02 at 30iterations 3.0994743E-05 4.9247742E-03 at 40iterations 2.8465245E-06 5.1116943E-04 at 50iterations finished qdiffx linear iterations at : 03:25:15 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 2.8465245E-06 5.1116943E-04 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 03:25:16 4.160u 0.298s 0:04.88 91.1% 0+0k 0+0io 6pf+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 Oct 11 2011 at 03:25:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2963 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: 1.680778 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): -28.85500 24.34300 ymin,ymax (A): -67.82401 -8.929000 zmin,zma (A): -25.21800 38.32400 x,y,z range (A): 53.19800 58.89500 63.54200 scale (grids/A): 1.680778 object centre (A): -2.256000 -38.37650 6.553000 number of atom coordinates read : 2963 total number of charged atoms : 2808 net assigned charge : -7.499990 assigned positive charge : 438.9932 centred at (gu) : 88.23278 95.45186 77.69106 assigned negative charge : -446.4945 centred at (gu) : 88.27401 95.50105 77.50974 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 67817 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29778 grid for indexing accessible points = 1.400000 m= 20193 mr = 43436 m= 2268 mr = 13355 m= 76 mr = 1113 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1412 time to turn everything in is 0.6000000 number of dielectric boundary points 32446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 21647 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) : 0.5602593 object centre at (A) : -2.256000 -38.37650 6.553000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1662334E-02 -8.6778002E-03 midg,1,midg; midg,igrid,midg -1.4399227E-02 -2.2419037E-02 1,midg,midg; igrid,midg,midg -2.7800612E-03 -9.5183012E-04 gauss-seidel spectral radius is 0.9982917 estimated iterations to convergence 192 setup time was (sec) 0.8900000 now iterating at: 03:25:17 rms-change max change #iterations 3.516158 162.8883 at 10iterations 1.500017 60.52863 at 20iterations 0.6430410 23.42631 at 30iterations 0.2748008 9.884018 at 40iterations 0.1176450 4.015007 at 50iterations 5.0051201E-02 1.850482 at 60iterations 2.1406917E-02 0.7310028 at 70iterations 9.1729034E-03 0.3295749 at 80iterations 3.9102160E-03 0.1307201 at 90iterations 1.6780612E-03 6.0851097E-02 at 100iterations 7.1543007E-04 2.4028897E-02 at 110iterations 3.0649759E-04 1.1375427E-02 at 120iterations finished qdiffx linear iterations at : 03:25:26 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 3.0649759E-04 1.1375427E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 03:25:26 9.610u 0.331s 0:10.40 95.5% 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 Oct 11 2011 at 03:25:26 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 = 2963 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: 2.521167 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): -28.85500 24.34300 ymin,ymax (A): -67.82401 -8.929000 zmin,zma (A): -25.21800 38.32400 x,y,z range (A): 53.19800 58.89500 63.54200 scale (grids/A): 2.521167 object centre (A): -2.256000 -38.37650 6.553000 number of atom coordinates read : 2963 total number of charged atoms : 2808 net assigned charge : -7.499990 assigned positive charge : 438.9932 centred at (gu) : 87.34892 98.17752 71.53631 assigned negative charge : -446.4945 centred at (gu) : 87.41084 98.25146 71.26465 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 157377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29778 grid for indexing accessible points = 1.400000 m= 69101 mr = 107109 m= 20177 mr = 52825 m= 3558 mr = 14886 m= 290 mr = 2365 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 4754 time to turn everything in is 1.480000 number of dielectric boundary points 73199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 22445 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) : 1.680778 object centre at (A) : -2.256000 -38.37650 6.553000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1371146 -0.2662201 midg,1,midg; midg,igrid,midg -0.2440167 -0.1613848 1,midg,midg; igrid,midg,midg -3.3632409E-02 -9.6571690E-04 gauss-seidel spectral radius is 0.9991777 estimated iterations to convergence 275 setup time was (sec) 1.800000 now iterating at: 03:25:28 rms-change max change #iterations 9.166581 285.9111 at 10iterations 5.271327 137.2841 at 20iterations 3.014858 83.18842 at 30iterations 1.711528 40.67543 at 40iterations 0.9664418 20.53151 at 50iterations 0.5454365 11.86173 at 60iterations 0.3065308 7.400412 at 70iterations 0.1717200 3.609894 at 80iterations 9.6160710E-02 2.184361 at 90iterations 5.3741187E-02 1.225800 at 100iterations 2.9986642E-02 0.7470436 at 110iterations 1.6760796E-02 0.3410864 at 120iterations 9.3402416E-03 0.1793644 at 130iterations 5.2213222E-03 0.1127853 at 140iterations 2.9116748E-03 5.7985306E-02 at 150iterations 1.6237734E-03 3.5453796E-02 at 160iterations 9.0412062E-04 1.7732143E-02 at 170iterations 5.0460320E-04 9.6532702E-03 at 180iterations finished qdiffx linear iterations at : 03:25:43 total time elapsed so far: 15.89000 # loops : 180 mean,max change (kT/e) : 5.0460320E-04 9.6532702E-03 energy calculations done at 15.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.08000 DelPhi exited at 03:25:43 16.082u 0.328s 0:16.74 97.9% 0+0k 0+0io 0pf+0w