Sat Oct 8 13:44:03 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 13:44:03 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 = 2454 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: 0.6313064 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): -11.94000 43.80000 ymin,ymax (A): -23.64300 17.51000 zmin,zma (A): -9.046000 47.34500 x,y,z range (A): 55.74000 41.15300 56.39100 scale (grids/A): 0.6313064 object centre (A): 15.93000 -3.066500 19.14950 number of atom coordinates read : 2454 total number of charged atoms : 2313 net assigned charge : 1.1116266E-05 assigned positive charge : 356.2094 centred at (gu) : 89.25645 90.28506 91.72800 assigned negative charge : -356.2098 centred at (gu) : 89.32954 90.32441 91.60509 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6565 nv = 96 ne = 84 npr = 50131 no. pairs analyzed = 50131 no. exposed pairs = 3048 no. arc points = 21285 no. surface atoms = 1044 nbur = 1410 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 3633 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2035 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7956 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3250410E-09 1.4631972E-08 midg,1,midg; midg,igrid,midg 2.8719369E-09 -3.7805283E-09 1,midg,midg; igrid,midg,midg 6.9068924E-09 -5.4488272E-09 gauss-seidel spectral radius is 0.9869911 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 13:44:04 rms-change max change #iterations 0.1301183 20.19606 at 10iterations 1.2685254E-02 1.767545 at 20iterations 1.4707487E-03 0.2195723 at 30iterations 2.7310295E-04 3.6542892E-02 at 40iterations 7.0195507E-05 9.6473694E-03 at 50iterations finished qdiffx linear iterations at : 13:44:07 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 7.0195507E-05 9.6473694E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 13:44:08 4.129u 0.305s 0:04.71 93.8% 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 Sat Oct 8 2011 at 13:44:08 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 = 2454 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: 1.893919 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): -11.94000 43.80000 ymin,ymax (A): -23.64300 17.51000 zmin,zma (A): -9.046000 47.34500 x,y,z range (A): 55.74000 41.15300 56.39100 scale (grids/A): 1.893919 object centre (A): 15.93000 -3.066500 19.14950 number of atom coordinates read : 2454 total number of charged atoms : 2313 net assigned charge : 1.1116266E-05 assigned positive charge : 356.2094 centred at (gu) : 87.76931 90.85493 95.18371 assigned negative charge : -356.2098 centred at (gu) : 87.98865 90.97292 94.81532 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 71772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21285 grid for indexing accessible points = 1.400000 m= 25313 mr = 50162 m= 3904 mr = 18422 m= 231 mr = 2330 m= 6 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 30241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18159 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) : 0.6313064 object centre at (A) : 15.93000 -3.066500 19.14950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2001063E-02 2.1516858E-02 midg,1,midg; midg,igrid,midg 5.5008172E-03 -1.1023307E-02 1,midg,midg; igrid,midg,midg 4.7044333E-02 -4.2350530E-03 gauss-seidel spectral radius is 0.9986071 estimated iterations to convergence 212 setup time was (sec) 0.9500000 now iterating at: 13:44:09 rms-change max change #iterations 3.983953 180.2528 at 10iterations 1.858462 68.84977 at 20iterations 0.8654712 27.01433 at 30iterations 0.4031607 13.88550 at 40iterations 0.1878671 6.056158 at 50iterations 8.7771505E-02 2.964287 at 60iterations 4.0899005E-02 1.349304 at 70iterations 1.9102156E-02 0.6045380 at 80iterations 8.9833671E-03 0.2756720 at 90iterations 4.2159576E-03 0.1407509 at 100iterations 2.0143874E-03 6.6256523E-02 at 110iterations 9.8245661E-04 3.1002998E-02 at 120iterations finished qdiffx linear iterations at : 13:44:18 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 9.8245661E-04 3.1002998E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 13:44:18 9.624u 0.323s 0:10.23 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 13:44:18 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 = 2454 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: 2.840879 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): -11.94000 43.80000 ymin,ymax (A): -23.64300 17.51000 zmin,zma (A): -9.046000 47.34500 x,y,z range (A): 55.74000 41.15300 56.39100 scale (grids/A): 2.840879 object centre (A): 15.93000 -3.066500 19.14950 number of atom coordinates read : 2454 total number of charged atoms : 2313 net assigned charge : 1.1116266E-05 assigned positive charge : 356.2094 centred at (gu) : 86.65382 91.28226 97.77540 assigned negative charge : -356.2098 centred at (gu) : 86.98292 91.45941 97.22279 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 166150 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21285 grid for indexing accessible points = 1.400000 m= 83383 mr = 121651 m= 29118 mr = 68083 m= 6870 mr = 23088 m= 993 mr = 4934 m= 52 mr = 620 m= 0 mr = 21 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 68169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 18504 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) : 1.893919 object centre at (A) : 15.93000 -3.066500 19.14950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1253899 0.3368154 midg,1,midg; midg,igrid,midg 5.7508610E-02 -0.1210230 1,midg,midg; igrid,midg,midg 1.023870 -4.8104376E-02 gauss-seidel spectral radius is 0.9992525 estimated iterations to convergence 289 setup time was (sec) 1.990000 now iterating at: 13:44:21 rms-change max change #iterations 9.435575 332.7732 at 10iterations 5.549085 128.5269 at 20iterations 3.236814 96.44131 at 30iterations 1.876822 39.00282 at 40iterations 1.087001 20.56118 at 50iterations 0.6281656 12.21656 at 60iterations 0.3621319 7.211185 at 70iterations 0.2085443 4.102444 at 80iterations 0.1203522 2.390840 at 90iterations 6.9075301E-02 1.304218 at 100iterations 3.9749768E-02 0.7333593 at 110iterations 2.2853399E-02 0.4036751 at 120iterations 1.3156652E-02 0.2527618 at 130iterations 7.5692497E-03 0.1493454 at 140iterations 4.3566222E-03 8.4026337E-02 at 150iterations 2.5202052E-03 4.7968864E-02 at 160iterations 1.4672106E-03 3.2081127E-02 at 170iterations 8.6442754E-04 1.6855240E-02 at 180iterations finished qdiffx linear iterations at : 13:44:35 total time elapsed so far: 15.95000 # loops : 180 mean,max change (kT/e) : 8.6442754E-04 1.6855240E-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 13:44:35 16.123u 0.324s 0:16.73 98.2% 0+0k 0+0io 0pf+0w