Wed Dec 21 14:21:36 PST 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 Wed Dec 21 2011 at 14:21:37 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1919 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 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: 0.6109071 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): -9.039000 49.23500 ymin,ymax (A): 8.652000 47.48300 zmin,zma (A): -3.712000 38.68000 x,y,z range (A): 58.27400 38.83100 42.39200 scale (grids/A): 0.6109071 object centre (A): 20.09800 28.06750 17.48400 number of atom coordinates read : 1919 total number of charged atoms : 1787 net assigned charge : -2.859995 assigned positive charge : 283.0400 centred at (gu) : 90.12160 89.74185 90.48182 assigned negative charge : -285.9003 centred at (gu) : 90.05774 89.72215 90.59679 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4861 nv = 96 ne = 84 npr = 39581 no. pairs analyzed = 39581 no. exposed pairs = 2407 no. arc points = 16702 no. surface atoms = 816 nbur = 1103 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 195 mr = 2668 m= 0 mr = 15 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 2373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1669 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2692646E-09 -6.7729617E-09 midg,1,midg; midg,igrid,midg -2.5944067E-09 -9.2449237E-10 1,midg,midg; igrid,midg,midg -4.0121173E-09 6.8526235E-10 gauss-seidel spectral radius is 0.9860697 estimated iterations to convergence 69 setup time was (sec) 0.3700000 now iterating at: 14:21:38 rms-change max change #iterations 0.1055156 16.89219 at 10iterations 9.2223752E-03 1.539431 at 20iterations 8.1206247E-04 0.1360855 at 30iterations 7.0459646E-05 1.1629105E-02 at 40iterations 6.2569634E-06 1.0757446E-03 at 50iterations finished qdiffx linear iterations at : 14:21:42 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 6.2569634E-06 1.0757446E-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) 4.090000 DelPhi exited at 14:21:58 4.089u 0.278s 0:21.63 20.1% 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 Wed Dec 21 2011 at 14:21:59 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1919 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 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: 1.832721 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): -9.039000 49.23500 ymin,ymax (A): 8.652000 47.48300 zmin,zma (A): -3.712000 38.68000 x,y,z range (A): 58.27400 38.83100 42.39200 scale (grids/A): 1.832721 object centre (A): 20.09800 28.06750 17.48400 number of atom coordinates read : 1919 total number of charged atoms : 1787 net assigned charge : -2.859995 assigned positive charge : 283.0400 centred at (gu) : 90.36458 89.22565 91.44565 assigned negative charge : -285.9003 centred at (gu) : 90.17364 89.16658 91.79057 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 52804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16702 grid for indexing accessible points = 1.400000 m= 17943 mr = 36394 m= 2158 mr = 13355 m= 55 mr = 1250 m= 0 mr = 9 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1288 time to turn everything in is 0.2600000 number of dielectric boundary points 21952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14037 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) : 0.6109071 object centre at (A) : 20.09800 28.06750 17.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1903759E-03 -1.1092720E-02 midg,1,midg; midg,igrid,midg -1.8094960E-03 -2.4090011E-03 1,midg,midg; igrid,midg,midg 9.0754898E-03 1.5198709E-02 gauss-seidel spectral radius is 0.9984464 estimated iterations to convergence 201 setup time was (sec) 0.5600000 now iterating at: 14:22:01 rms-change max change #iterations 3.321353 168.8436 at 10iterations 1.479677 54.72710 at 20iterations 0.6590636 25.18155 at 30iterations 0.2932811 11.24770 at 40iterations 0.1305227 5.290039 at 50iterations 5.7951234E-02 2.184092 at 60iterations 2.5807235E-02 0.9270318 at 70iterations 1.1488102E-02 0.4526310 at 80iterations 5.1147300E-03 0.1875954 at 90iterations 2.2732525E-03 8.2376659E-02 at 100iterations 1.0162970E-03 3.6795139E-02 at 110iterations 4.5241046E-04 2.0028114E-02 at 120iterations finished qdiffx linear iterations at : 14:22:10 total time elapsed so far: 9.970000 # loops : 120 mean,max change (kT/e) : 4.5241046E-04 2.0028114E-02 energy calculations done at 9.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 14:22:25 10.120u 0.336s 0:26.07 40.0% 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 Wed Dec 21 2011 at 14:22:27 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1919 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 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: 2.749082 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): -9.039000 49.23500 ymin,ymax (A): 8.652000 47.48300 zmin,zma (A): -3.712000 38.68000 x,y,z range (A): 58.27400 38.83100 42.39200 scale (grids/A): 2.749082 object centre (A): 20.09800 28.06750 17.48400 number of atom coordinates read : 1919 total number of charged atoms : 1787 net assigned charge : -2.859995 assigned positive charge : 283.0400 centred at (gu) : 90.54690 88.83843 92.16846 assigned negative charge : -285.9003 centred at (gu) : 90.26041 88.75000 92.68583 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 122105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16702 grid for indexing accessible points = 1.400000 m= 60157 mr = 88011 m= 19524 mr = 49543 m= 3609 mr = 15782 m= 280 mr = 2705 m= 3 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 4464 time to turn everything in is 0.6600000 number of dielectric boundary points 49505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 14296 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) : 1.832721 object centre at (A) : 20.09800 28.06750 17.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4864477E-02 -9.0957195E-02 midg,1,midg; midg,igrid,midg 1.1381367E-02 -1.8762993E-02 1,midg,midg; igrid,midg,midg 0.2099564 0.2472080 gauss-seidel spectral radius is 0.9991886 estimated iterations to convergence 277 setup time was (sec) 0.9500000 now iterating at: 14:22:29 rms-change max change #iterations 7.932431 340.8215 at 10iterations 4.478567 137.1979 at 20iterations 2.513765 56.97174 at 30iterations 1.406975 32.30132 at 40iterations 0.7897044 17.34792 at 50iterations 0.4406052 9.383831 at 60iterations 0.2455741 6.243362 at 70iterations 0.1372509 3.010986 at 80iterations 7.6481521E-02 1.653633 at 90iterations 4.2761743E-02 0.9424210 at 100iterations 2.3882370E-02 0.5302963 at 110iterations 1.3330504E-02 0.2849264 at 120iterations 7.4445168E-03 0.1675224 at 130iterations 4.1588889E-03 9.0072632E-02 at 140iterations 2.3164779E-03 4.9547672E-02 at 150iterations 1.2947548E-03 2.6878357E-02 at 160iterations 7.2173710E-04 1.6075134E-02 at 170iterations 4.0322822E-04 8.7966919E-03 at 180iterations finished qdiffx linear iterations at : 14:22:42 total time elapsed so far: 13.70000 # loops : 180 mean,max change (kT/e) : 4.0322822E-04 8.7966919E-03 energy calculations done at 13.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.84000 DelPhi exited at 14:22:51 13.839u 0.337s 0:24.20 58.5% 0+0k 0+0io 0pf+0w