Sun Oct 9 19:03:21 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 Sun Oct 9 2011 at 19:03:21 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5181 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5492048 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): 3.300000 68.12100 ymin,ymax (A): -8.985000 53.39600 zmin,zma (A): -2.644000 61.63600 x,y,z range (A): 64.82100 62.38100 64.28000 scale (grids/A): 0.5492048 object centre (A): 35.71050 22.20550 29.49600 number of atom coordinates read : 5181 total number of charged atoms : 5036 net assigned charge : 0.6210560 assigned positive charge : 795.3494 centred at (gu) : 87.87852 89.29762 89.86040 assigned negative charge : -794.7346 centred at (gu) : 87.76665 89.32051 89.83761 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 10195 nv = 96 ne = 84 npr = 104895 no. pairs analyzed = 104895 no. exposed pairs = 5992 no. arc points = 40983 no. surface atoms = 2055 nbur = 3126 mkacc time = 0.2200000 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 = 1.568000 m= 451 mr = 5842 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4230 ## 485 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 13439 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3449598E-10 3.6709416E-10 midg,1,midg; midg,igrid,midg 4.5463913E-10 -1.9079753E-10 1,midg,midg; igrid,midg,midg -2.4558129E-09 9.1554148E-10 gauss-seidel spectral radius is 0.9830639 estimated iterations to convergence 63 setup time was (sec) 0.6800000 now iterating at: 19:03:22 rms-change max change #iterations 0.1040488 13.09955 at 10iterations 9.5257787E-03 1.212482 at 20iterations 2.7848866E-03 0.3433228 at 30iterations 1.2735303E-03 0.1617047 at 40iterations 6.0183840E-04 7.9942226E-02 at 50iterations finished qdiffx linear iterations at : 19:03:24 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 6.0183840E-04 7.9942226E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 19:03:25 3.257u 0.165s 0:03.71 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 Sun Oct 9 2011 at 19:03:25 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5181 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.647614 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): 3.300000 68.12100 ymin,ymax (A): -8.985000 53.39600 zmin,zma (A): -2.644000 61.63600 x,y,z range (A): 64.82100 62.38100 64.28000 scale (grids/A): 1.647614 object centre (A): 35.71050 22.20550 29.49600 number of atom coordinates read : 5181 total number of charged atoms : 5036 net assigned charge : 0.6210560 assigned positive charge : 795.3494 centred at (gu) : 83.63389 87.89156 89.57991 assigned negative charge : -794.7346 centred at (gu) : 83.29991 87.96159 89.51279 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 113987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40983 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38934 mr = 82747 m= 4520 mr = 28265 m= 143 mr = 2333 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 44216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 438 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 38686 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) : 0.5492048 object centre at (A) : 35.71050 22.20550 29.49600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4577219E-02 -1.4553188E-02 midg,1,midg; midg,igrid,midg 2.0180356E-02 8.0490634E-03 1,midg,midg; igrid,midg,midg -2.7323952E-02 1.5288053E-02 gauss-seidel spectral radius is 0.9984173 estimated iterations to convergence 199 setup time was (sec) 1.020000 now iterating at: 19:03:26 rms-change max change #iterations 4.805726 159.8441 at 10iterations 2.122670 63.33129 at 20iterations 0.9398130 24.85078 at 30iterations 0.4159184 12.43180 at 40iterations 0.1847994 5.317273 at 50iterations 8.2256578E-02 2.170594 at 60iterations 3.6852412E-02 1.194082 at 70iterations 1.6870448E-02 0.5248566 at 80iterations 8.1696361E-03 0.2198346 at 90iterations 4.3702391E-03 0.1287766 at 100iterations 2.6766555E-03 7.4190140E-02 at 110iterations 1.8486726E-03 4.8374176E-02 at 120iterations finished qdiffx linear iterations at : 19:03:32 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 1.8486726E-03 4.8374176E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 19:03:32 7.153u 0.160s 0:07.59 96.3% 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 Sun Oct 9 2011 at 19:03:32 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5181 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.471421 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): 3.300000 68.12100 ymin,ymax (A): -8.985000 53.39600 zmin,zma (A): -2.644000 61.63600 x,y,z range (A): 64.82100 62.38100 64.28000 scale (grids/A): 2.471421 object centre (A): 35.71050 22.20550 29.49600 number of atom coordinates read : 5181 total number of charged atoms : 5036 net assigned charge : 0.6210560 assigned positive charge : 795.3494 centred at (gu) : 80.45060 86.83708 89.36948 assigned negative charge : -794.7346 centred at (gu) : 79.94972 86.94246 89.26894 start vw surface at 0.1900000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 264757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40983 grid for indexing accessible points = 1.400000 m= 132650 mr = 201124 m= 41108 mr = 108406 m= 7362 mr = 31857 m= 636 mr = 5066 m= 14 mr = 334 m= 0 mr = 4 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 99736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 40246 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) : 1.647614 object centre at (A) : 35.71050 22.20550 29.49600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2781810 -0.3472477 midg,1,midg; midg,igrid,midg 0.1400879 -5.1903687E-02 1,midg,midg; igrid,midg,midg -0.4777713 0.2148815 gauss-seidel spectral radius is 0.9992509 estimated iterations to convergence 288 setup time was (sec) 2.090000 now iterating at: 19:03:34 rms-change max change #iterations 12.22442 308.3848 at 10iterations 7.194808 190.1713 at 20iterations 4.220267 82.73933 at 30iterations 2.466283 45.69945 at 40iterations 1.429642 26.32240 at 50iterations 0.8299507 14.16613 at 60iterations 0.4789877 8.308849 at 70iterations 0.2764458 4.574181 at 80iterations 0.1593386 2.740514 at 90iterations 9.2000619E-02 1.517427 at 100iterations 5.3042546E-02 0.9175129 at 110iterations 3.0734051E-02 0.5148239 at 120iterations 1.7919485E-02 0.3059235 at 130iterations 1.0628124E-02 0.1790619 at 140iterations 6.4861723E-03 0.1163368 at 150iterations 4.1507091E-03 7.8804970E-02 at 160iterations 2.8428398E-03 5.1000595E-02 at 170iterations 2.0889619E-03 3.7183762E-02 at 180iterations finished qdiffx linear iterations at : 19:03:44 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 2.0889619E-03 3.7183762E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 19:03:45 11.897u 0.183s 0:12.36 97.6% 0+0k 0+0io 0pf+0w