Tue Oct 11 08:37:25 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 08:37:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2068 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: 0.7065595 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): 19.00600 64.42600 ymin,ymax (A): -3.438000 33.50500 zmin,zma (A): 20.24200 70.62700 x,y,z range (A): 45.42000 36.94300 50.38500 scale (grids/A): 0.7065595 object centre (A): 41.71600 15.03350 45.43450 number of atom coordinates read : 2068 total number of charged atoms : 1940 net assigned charge : 6.500009 assigned positive charge : 314.1260 centred at (gu) : 89.89731 89.69604 89.64231 assigned negative charge : -307.6262 centred at (gu) : 90.03719 89.72447 89.59425 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7033 nv = 96 ne = 84 npr = 41800 no. pairs analyzed = 41800 no. exposed pairs = 2511 no. arc points = 17164 no. surface atoms = 850 nbur = 1218 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4085 m= 4 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1603 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7811 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2684383E-08 7.1551867E-08 midg,1,midg; midg,igrid,midg 7.1319811E-08 3.7934164E-08 1,midg,midg; igrid,midg,midg 1.2212671E-07 -1.3738673E-08 gauss-seidel spectral radius is 0.9895572 estimated iterations to convergence 80 setup time was (sec) 0.6000000 now iterating at: 08:37:26 rms-change max change #iterations 0.1984571 32.08687 at 10iterations 2.4122452E-02 3.735802 at 20iterations 3.0582314E-03 0.4171550 at 30iterations 4.4720105E-04 6.0859680E-02 at 40iterations 8.6859865E-05 1.1024475E-02 at 50iterations finished qdiffx linear iterations at : 08:37:29 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 8.6859865E-05 1.1024475E-02 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 08:37:30 3.987u 0.165s 0:04.64 89.2% 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 08:37:30 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 = 2068 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: 2.119678 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): 19.00600 64.42600 ymin,ymax (A): -3.438000 33.50500 zmin,zma (A): 20.24200 70.62700 x,y,z range (A): 45.42000 36.94300 50.38500 scale (grids/A): 2.119678 object centre (A): 41.71600 15.03350 45.43450 number of atom coordinates read : 2068 total number of charged atoms : 1940 net assigned charge : 6.500009 assigned positive charge : 314.1260 centred at (gu) : 89.69186 89.08803 88.92690 assigned negative charge : -307.6262 centred at (gu) : 90.11163 89.17350 88.78279 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17164 grid for indexing accessible points = 1.400000 m= 30526 mr = 53197 m= 6020 mr = 23352 m= 580 mr = 4047 m= 13 mr = 335 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 0.7100000 number of dielectric boundary points 30665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15414 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) : 0.7065595 object centre at (A) : 41.71600 15.03350 45.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1568807E-02 4.5060713E-02 midg,1,midg; midg,igrid,midg 2.8975181E-02 9.8136319E-03 1,midg,midg; igrid,midg,midg 3.5399884E-02 2.0634793E-02 gauss-seidel spectral radius is 0.9988266 estimated iterations to convergence 231 setup time was (sec) 1.030000 now iterating at: 08:37:31 rms-change max change #iterations 4.560486 195.2401 at 10iterations 2.259335 73.46284 at 20iterations 1.117684 38.41206 at 30iterations 0.5551489 16.67160 at 40iterations 0.2750196 8.302284 at 50iterations 0.1367903 4.002583 at 60iterations 6.7846343E-02 2.179096 at 70iterations 3.3707671E-02 0.9799709 at 80iterations 1.6744519E-02 0.5379777 at 90iterations 8.3811693E-03 0.2988129 at 100iterations 4.1967724E-03 0.1263804 at 110iterations 2.1225568E-03 6.1969757E-02 at 120iterations finished qdiffx linear iterations at : 08:37:38 total time elapsed so far: 8.670000 # loops : 120 mean,max change (kT/e) : 2.1225568E-03 6.1969757E-02 energy calculations done at 8.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.900000 DelPhi exited at 08:37:39 8.904u 0.200s 0:09.49 95.8% 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 08:37:39 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 = 2068 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: 3.179518 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): 19.00600 64.42600 ymin,ymax (A): -3.438000 33.50500 zmin,zma (A): 20.24200 70.62700 x,y,z range (A): 45.42000 36.94300 50.38500 scale (grids/A): 3.179518 object centre (A): 41.71600 15.03350 45.43450 number of atom coordinates read : 2068 total number of charged atoms : 1940 net assigned charge : 6.500009 assigned positive charge : 314.1260 centred at (gu) : 89.53797 88.63197 88.39038 assigned negative charge : -307.6262 centred at (gu) : 90.16753 88.76023 88.17420 start vw surface at 0.1700000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 171408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17164 grid for indexing accessible points = 1.400000 m= 94614 mr = 127407 m= 39091 mr = 79345 m= 11434 mr = 32454 m= 2422 mr = 8820 m= 287 mr = 1877 m= 2 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.230000 number of dielectric boundary points 69158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 15520 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) : 2.119678 object centre at (A) : 41.71600 15.03350 45.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2349649 0.3793154 midg,1,midg; midg,igrid,midg 0.2252877 7.4217804E-02 1,midg,midg; igrid,midg,midg 0.2955821 0.3547054 gauss-seidel spectral radius is 0.9992922 estimated iterations to convergence 297 setup time was (sec) 2.580000 now iterating at: 08:37:42 rms-change max change #iterations 10.16220 388.0232 at 10iterations 5.980553 117.9647 at 20iterations 3.521476 64.43181 at 30iterations 2.071112 39.35867 at 40iterations 1.215493 22.02182 at 50iterations 0.7111654 14.73447 at 60iterations 0.4166666 7.754230 at 70iterations 0.2434649 4.099874 at 80iterations 0.1426372 2.548107 at 90iterations 8.3317086E-02 1.466674 at 100iterations 4.8691995E-02 0.9148502 at 110iterations 2.8589234E-02 0.5012991 at 120iterations 1.6829573E-02 0.2989016 at 130iterations 9.9976324E-03 0.1810005 at 140iterations 6.0269735E-03 0.1148957 at 150iterations 3.7226996E-03 6.7577362E-02 at 160iterations 2.3966690E-03 4.3874741E-02 at 170iterations 1.6265149E-03 3.1948090E-02 at 180iterations finished qdiffx linear iterations at : 08:37:54 total time elapsed so far: 14.85000 # loops : 180 mean,max change (kT/e) : 1.6265149E-03 3.1948090E-02 energy calculations done at 14.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.09000 DelPhi exited at 08:37:56 15.093u 0.207s 0:16.48 92.7% 0+0k 0+0io 0pf+0w