Sat Oct 8 13:38:47 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 Sat Oct 8 2011 at 13:38:47 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3046 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! 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: 0.6117469 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): -12.98400 33.81700 ymin,ymax (A): -12.82000 45.37400 zmin,zma (A): -41.14300 11.54200 x,y,z range (A): 46.80100 58.19400 52.68500 scale (grids/A): 0.6117469 object centre (A): 10.41650 16.27700 -14.80050 number of atom coordinates read : 3046 total number of charged atoms : 2899 net assigned charge : 1.4008060E-02 assigned positive charge : 458.1526 centred at (gu) : 91.02128 92.11530 91.09347 assigned negative charge : -458.1393 centred at (gu) : 91.07404 92.02372 91.17042 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 64082 no. pairs analyzed = 64082 no. exposed pairs = 3480 no. arc points = 24519 no. surface atoms = 1186 nbur = 1860 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 4239 m= 3 mr = 37 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 0.4100000 number of dielectric boundary points 3493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2391 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9318 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6224224E-09 -6.1220642E-09 midg,1,midg; midg,igrid,midg -3.5311047E-09 8.9697823E-09 1,midg,midg; igrid,midg,midg 2.5254248E-09 -4.1268056E-09 gauss-seidel spectral radius is 0.9861949 estimated iterations to convergence 70 setup time was (sec) 0.6900000 now iterating at: 13:38:48 rms-change max change #iterations 0.1328174 21.44916 at 10iterations 1.2244352E-02 1.560022 at 20iterations 1.2236373E-03 0.1748505 at 30iterations 1.5250604E-04 2.1253586E-02 at 40iterations 2.5931624E-05 4.1561127E-03 at 50iterations finished qdiffx linear iterations at : 13:38:51 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 2.5931624E-05 4.1561127E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 13:38:52 4.216u 0.253s 0:04.77 93.5% 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 Sat Oct 8 2011 at 13:38:52 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3046 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! 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: 1.835241 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): -12.98400 33.81700 ymin,ymax (A): -12.82000 45.37400 zmin,zma (A): -41.14300 11.54200 x,y,z range (A): 46.80100 58.19400 52.68500 scale (grids/A): 1.835241 object centre (A): 10.41650 16.27700 -14.80050 number of atom coordinates read : 3046 total number of charged atoms : 2899 net assigned charge : 1.4008060E-02 assigned positive charge : 458.1526 centred at (gu) : 93.06324 96.34510 93.27995 assigned negative charge : -458.1393 centred at (gu) : 93.22182 96.07079 93.51095 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 81586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24519 grid for indexing accessible points = 1.400000 m= 27862 mr = 58607 m= 3596 mr = 20414 m= 152 mr = 2066 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 121 time to turn everything in is 0.7300000 number of dielectric boundary points 32094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 22737 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) : 0.6117469 object centre at (A) : 10.41650 16.27700 -14.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5834106E-02 7.9894606E-03 midg,1,midg; midg,igrid,midg -1.8378977E-02 3.2774106E-02 1,midg,midg; igrid,midg,midg 7.4393484E-03 -4.5221448E-03 gauss-seidel spectral radius is 0.9985670 estimated iterations to convergence 209 setup time was (sec) 1.040000 now iterating at: 13:38:53 rms-change max change #iterations 4.349271 171.6075 at 10iterations 2.008132 71.44462 at 20iterations 0.9258109 30.14001 at 30iterations 0.4253299 12.76940 at 40iterations 0.1965926 5.727386 at 50iterations 9.0503857E-02 2.565174 at 60iterations 4.1575819E-02 1.292280 at 70iterations 1.9232290E-02 0.5886593 at 80iterations 8.8808611E-03 0.2939356 at 90iterations 4.0818411E-03 0.1232433 at 100iterations 1.8807191E-03 5.7556152E-02 at 110iterations 8.7377074E-04 3.0668259E-02 at 120iterations finished qdiffx linear iterations at : 13:39:02 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 8.7377074E-04 3.0668259E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 13:39:02 9.711u 0.305s 0:10.43 95.9% 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 13:39:02 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3046 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! 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: 2.752861 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): -12.98400 33.81700 ymin,ymax (A): -12.82000 45.37400 zmin,zma (A): -41.14300 11.54200 x,y,z range (A): 46.80100 58.19400 52.68500 scale (grids/A): 2.752861 object centre (A): 10.41650 16.27700 -14.80050 number of atom coordinates read : 3046 total number of charged atoms : 2899 net assigned charge : 1.4008060E-02 assigned positive charge : 458.1526 centred at (gu) : 94.59473 99.51765 94.91973 assigned negative charge : -458.1393 centred at (gu) : 94.83266 99.10616 95.26637 start vw surface at 0.1600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 189633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24519 grid for indexing accessible points = 1.400000 m= 93600 mr = 142288 m= 30396 mr = 77032 m= 6189 mr = 23983 m= 646 mr = 4461 m= 19 mr = 356 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 1.800000 number of dielectric boundary points 72362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 23191 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) : 1.835241 object centre at (A) : 10.41650 16.27700 -14.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1604790 0.2139397 midg,1,midg; midg,igrid,midg -0.1352537 0.5317792 1,midg,midg; igrid,midg,midg 0.1006928 -2.3595469E-02 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 2.130000 now iterating at: 13:39:05 rms-change max change #iterations 10.31708 325.1081 at 10iterations 6.011216 150.3277 at 20iterations 3.473204 78.51072 at 30iterations 2.002113 44.25964 at 40iterations 1.150264 22.69888 at 50iterations 0.6613070 12.89124 at 60iterations 0.3788048 8.175254 at 70iterations 0.2176318 4.087595 at 80iterations 0.1246042 2.240345 at 90iterations 7.1466044E-02 1.241384 at 100iterations 4.0888779E-02 0.7001426 at 110iterations 2.3395374E-02 0.4186983 at 120iterations 1.3407227E-02 0.2434540 at 130iterations 7.6678121E-03 0.1306458 at 140iterations 4.3917205E-03 7.7009201E-02 at 150iterations 2.5247426E-03 4.2625427E-02 at 160iterations 1.4517125E-03 2.6229858E-02 at 170iterations 8.3608838E-04 1.4766693E-02 at 180iterations finished qdiffx linear iterations at : 13:39:19 total time elapsed so far: 16.31000 # loops : 180 mean,max change (kT/e) : 8.3608838E-04 1.4766693E-02 energy calculations done at 16.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.50000 DelPhi exited at 13:39:19 16.503u 0.342s 0:17.21 97.8% 0+0k 0+0io 0pf+0w