Mon Oct 10 19:37:16 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 Mon Oct 10 2011 at 19:37:16 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 = 3213 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: 0.5973154 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): -6.982000 51.38400 ymin,ymax (A): 37.46800 94.78400 zmin,zma (A): -20.40300 39.19700 x,y,z range (A): 58.36600 57.31601 59.60000 scale (grids/A): 0.5973154 object centre (A): 22.20100 66.12600 9.397001 number of atom coordinates read : 3213 total number of charged atoms : 3074 net assigned charge : 5.500014 assigned positive charge : 488.1058 centred at (gu) : 90.23389 90.78044 91.56526 assigned negative charge : -482.6068 centred at (gu) : 90.21116 90.91302 91.55515 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7627 nv = 96 ne = 84 npr = 64420 no. pairs analyzed = 64420 no. exposed pairs = 4233 no. arc points = 29554 no. surface atoms = 1426 nbur = 1787 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 3957 m= 3 mr = 26 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 0.3300000 number of dielectric boundary points 4042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3009 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2640042E-09 3.7152599E-09 midg,1,midg; midg,igrid,midg 6.3834271E-09 -4.1127497E-09 1,midg,midg; igrid,midg,midg 1.1852522E-09 3.3059062E-09 gauss-seidel spectral radius is 0.9855502 estimated iterations to convergence 68 setup time was (sec) 0.5300000 now iterating at: 19:37:16 rms-change max change #iterations 0.1186503 18.77938 at 10iterations 9.8869726E-03 1.537637 at 20iterations 8.3520066E-04 0.1175804 at 30iterations 7.1142691E-05 1.1723042E-02 at 40iterations 6.0337743E-06 9.6130371E-04 at 50iterations finished qdiffx linear iterations at : 19:37:19 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 6.0337743E-06 9.6130371E-04 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 19:37:20 3.139u 0.165s 0:03.75 87.7% 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 Mon Oct 10 2011 at 19:37:20 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 = 3213 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.791946 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): -6.982000 51.38400 ymin,ymax (A): 37.46800 94.78400 zmin,zma (A): -20.40300 39.19700 x,y,z range (A): 58.36600 57.31601 59.60000 scale (grids/A): 1.791946 object centre (A): 22.20100 66.12600 9.397001 number of atom coordinates read : 3213 total number of charged atoms : 3074 net assigned charge : 5.500014 assigned positive charge : 488.1058 centred at (gu) : 90.70086 92.34048 94.69485 assigned negative charge : -482.6068 centred at (gu) : 90.63303 92.73853 94.66510 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29554 grid for indexing accessible points = 1.400000 m= 28689 mr = 55567 m= 3966 mr = 20249 m= 205 mr = 2209 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.5900000 number of dielectric boundary points 37239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 23961 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) : 0.5973154 object centre at (A) : 22.20100 66.12600 9.397001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0124634E-02 -7.7177617E-03 midg,1,midg; midg,igrid,midg 3.4876149E-02 1.4507145E-03 1,midg,midg; igrid,midg,midg 3.2553799E-02 -3.2142739E-04 gauss-seidel spectral radius is 0.9985248 estimated iterations to convergence 206 setup time was (sec) 0.8700000 now iterating at: 19:37:21 rms-change max change #iterations 4.230620 188.4458 at 10iterations 1.912581 66.51357 at 20iterations 0.8692810 28.15308 at 30iterations 0.3929011 11.60250 at 40iterations 0.1790640 6.188633 at 50iterations 8.1150651E-02 2.589242 at 60iterations 3.6876209E-02 1.210960 at 70iterations 1.6678384E-02 0.5301694 at 80iterations 7.5847539E-03 0.2505188 at 90iterations 3.4450623E-03 0.1040907 at 100iterations 1.5655484E-03 4.6243429E-02 at 110iterations 7.1361131E-04 2.2809982E-02 at 120iterations finished qdiffx linear iterations at : 19:37:27 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 7.1361131E-04 2.2809982E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 19:37:28 7.520u 0.250s 0:08.44 92.0% 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 Mon Oct 10 2011 at 19:37:28 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 = 3213 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: 2.687919 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): -6.982000 51.38400 ymin,ymax (A): 37.46800 94.78400 zmin,zma (A): -20.40300 39.19700 x,y,z range (A): 58.36600 57.31601 59.60000 scale (grids/A): 2.687919 object centre (A): 22.20100 66.12600 9.397001 number of atom coordinates read : 3213 total number of charged atoms : 3074 net assigned charge : 5.500014 assigned positive charge : 488.1058 centred at (gu) : 91.05110 93.51057 97.04227 assigned negative charge : -482.6068 centred at (gu) : 90.94952 94.10773 96.99770 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 190678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29554 grid for indexing accessible points = 1.400000 m= 94068 mr = 135451 m= 31985 mr = 74982 m= 6814 mr = 24814 m= 852 mr = 4664 m= 38 mr = 501 m= 0 mr = 1 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 619 time to turn everything in is 1.480000 number of dielectric boundary points 84022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 24584 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) : 1.791946 object centre at (A) : 22.20100 66.12600 9.397001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1520600 -0.1114757 midg,1,midg; midg,igrid,midg 0.4434454 4.2108957E-02 1,midg,midg; igrid,midg,midg 0.4894235 -0.1079769 gauss-seidel spectral radius is 0.9992482 estimated iterations to convergence 288 setup time was (sec) 1.800000 now iterating at: 19:37:30 rms-change max change #iterations 10.36813 263.3977 at 10iterations 6.077815 140.5318 at 20iterations 3.527609 68.72368 at 30iterations 2.040489 39.68229 at 40iterations 1.176487 22.09101 at 50iterations 0.6763161 13.24178 at 60iterations 0.3877170 7.246647 at 70iterations 0.2224770 4.261006 at 80iterations 0.1277192 2.328135 at 90iterations 7.3239587E-02 1.299102 at 100iterations 4.1847661E-02 0.7827682 at 110iterations 2.3906998E-02 0.4595846 at 120iterations 1.3685058E-02 0.2463236 at 130iterations 7.8249667E-03 0.1466560 at 140iterations 4.4743358E-03 9.4736099E-02 at 150iterations 2.5532576E-03 4.6500862E-02 at 160iterations 1.4636826E-03 2.5436401E-02 at 170iterations 8.3539804E-04 1.6325474E-02 at 180iterations finished qdiffx linear iterations at : 19:37:41 total time elapsed so far: 12.36000 # loops : 180 mean,max change (kT/e) : 8.3539804E-04 1.6325474E-02 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 19:37:42 12.538u 0.234s 0:13.55 94.1% 0+0k 0+0io 0pf+0w