Tue Oct 11 08:33:33 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 08:33:33 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 = 2644 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: 0.6403108 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): -65.72200 -14.52900 ymin,ymax (A): -46.43200 0.6339999 zmin,zma (A): 4.571000 60.16900 x,y,z range (A): 51.19300 47.06600 55.59800 scale (grids/A): 0.6403108 object centre (A): -40.12550 -22.89900 32.37000 number of atom coordinates read : 2644 total number of charged atoms : 2501 net assigned charge : 11.00003 assigned positive charge : 400.9749 centred at (gu) : 89.32865 89.57790 91.40456 assigned negative charge : -389.9755 centred at (gu) : 89.32475 89.30783 91.35916 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7145 nv = 96 ne = 84 npr = 53465 no. pairs analyzed = 53465 no. exposed pairs = 3170 no. arc points = 21972 no. surface atoms = 1072 nbur = 1572 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3961 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2266 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2089651E-09 2.9005500E-08 midg,1,midg; midg,igrid,midg -1.8257673E-08 4.3094708E-08 1,midg,midg; igrid,midg,midg 1.8127313E-08 1.4539367E-08 gauss-seidel spectral radius is 0.9873629 estimated iterations to convergence 73 setup time was (sec) 0.5100000 now iterating at: 08:33:34 rms-change max change #iterations 0.1466313 19.84796 at 10iterations 1.4496182E-02 2.346717 at 20iterations 1.4312003E-03 0.1945877 at 30iterations 1.4400731E-04 1.9332886E-02 at 40iterations 1.5818197E-05 2.2201538E-03 at 50iterations finished qdiffx linear iterations at : 08:33:36 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.5818197E-05 2.2201538E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 08:33:37 3.129u 0.137s 0:03.60 90.2% 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 08:33:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 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: 1.920932 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): -65.72200 -14.52900 ymin,ymax (A): -46.43200 0.6339999 zmin,zma (A): 4.571000 60.16900 x,y,z range (A): 51.19300 47.06600 55.59800 scale (grids/A): 1.920932 object centre (A): -40.12550 -22.89900 32.37000 number of atom coordinates read : 2644 total number of charged atoms : 2501 net assigned charge : 11.00003 assigned positive charge : 400.9749 centred at (gu) : 87.98552 88.73297 94.21328 assigned negative charge : -389.9755 centred at (gu) : 87.97407 87.92319 94.07726 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21972 grid for indexing accessible points = 1.400000 m= 28639 mr = 53487 m= 4596 mr = 21468 m= 237 mr = 2921 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 31932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19670 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) : 0.6403108 object centre at (A) : -40.12550 -22.89900 32.37000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2542337E-02 4.9648926E-02 midg,1,midg; midg,igrid,midg -1.2885346E-02 5.8779728E-02 1,midg,midg; igrid,midg,midg 2.0393725E-02 -5.5693551E-03 gauss-seidel spectral radius is 0.9986598 estimated iterations to convergence 216 setup time was (sec) 0.8500000 now iterating at: 08:33:38 rms-change max change #iterations 4.334719 203.7346 at 10iterations 2.045835 71.87373 at 20iterations 0.9688426 32.64082 at 30iterations 0.4565160 16.76673 at 40iterations 0.2160685 7.608150 at 50iterations 0.1020208 3.401611 at 60iterations 4.8294228E-02 1.670616 at 70iterations 2.2847511E-02 0.7480078 at 80iterations 1.0776658E-02 0.3332663 at 90iterations 5.1037981E-03 0.1581841 at 100iterations 2.4133564E-03 8.3137512E-02 at 110iterations 1.1406536E-03 3.5224915E-02 at 120iterations finished qdiffx linear iterations at : 08:33:44 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 1.1406536E-03 3.5224915E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 08:33:44 6.985u 0.162s 0:07.51 95.0% 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 Tue Oct 11 2011 at 08:33:45 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 = 2644 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: 2.881398 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): -65.72200 -14.52900 ymin,ymax (A): -46.43200 0.6339999 zmin,zma (A): 4.571000 60.16900 x,y,z range (A): 51.19300 47.06600 55.59800 scale (grids/A): 2.881398 object centre (A): -40.12550 -22.89900 32.37000 number of atom coordinates read : 2644 total number of charged atoms : 2501 net assigned charge : 11.00003 assigned positive charge : 400.9749 centred at (gu) : 86.97811 88.09915 96.31971 assigned negative charge : -389.9755 centred at (gu) : 86.96111 86.88477 96.11583 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 176501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21972 grid for indexing accessible points = 1.400000 m= 91439 mr = 129258 m= 34485 mr = 75427 m= 8092 mr = 28102 m= 1022 mr = 6083 m= 48 mr = 643 m= 0 mr = 16 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 72058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 20008 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) : 1.920932 object centre at (A) : -40.12550 -22.89900 32.37000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2919572 0.1599341 midg,1,midg; midg,igrid,midg -0.1209643 0.5322303 1,midg,midg; igrid,midg,midg 9.6941501E-02 -3.3039089E-02 gauss-seidel spectral radius is 0.9992626 estimated iterations to convergence 291 setup time was (sec) 1.640000 now iterating at: 08:33:47 rms-change max change #iterations 10.13390 412.9615 at 10iterations 5.956123 144.8800 at 20iterations 3.477278 81.82727 at 30iterations 2.020083 42.53616 at 40iterations 1.177389 25.21665 at 50iterations 0.6834759 15.31581 at 60iterations 0.3949091 7.642506 at 70iterations 0.2288366 4.390537 at 80iterations 0.1321690 2.530554 at 90iterations 7.6203458E-02 1.390259 at 100iterations 4.4032868E-02 0.8193150 at 110iterations 2.5392557E-02 0.4836731 at 120iterations 1.4655273E-02 0.2494192 at 130iterations 8.4671918E-03 0.1542959 at 140iterations 4.8698741E-03 8.4609985E-02 at 150iterations 2.8021801E-03 4.9859047E-02 at 160iterations 1.6185523E-03 2.9669762E-02 at 170iterations 9.3063927E-04 1.7358780E-02 at 180iterations finished qdiffx linear iterations at : 08:33:56 total time elapsed so far: 11.12000 # loops : 180 mean,max change (kT/e) : 9.3063927E-04 1.7358780E-02 energy calculations done at 11.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 08:33:57 11.293u 0.169s 0:12.21 93.7% 0+0k 0+0io 0pf+0w