Sat Oct 8 14:41:27 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 Sat Oct 8 2011 at 14:41:27 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.5952679 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): -14.24100 35.98100 ymin,ymax (A): -14.40800 45.39700 zmin,zma (A): -40.84800 11.77500 x,y,z range (A): 50.22200 59.80500 52.62300 scale (grids/A): 0.5952679 object centre (A): 10.87000 15.49450 -14.53650 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 7.1674585E-06 assigned positive charge : 453.7835 centred at (gu) : 91.37377 92.23177 91.10123 assigned negative charge : -453.7843 centred at (gu) : 91.41531 92.14547 91.16006 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6938 nv = 96 ne = 84 npr = 63874 no. pairs analyzed = 63874 no. exposed pairs = 3449 no. arc points = 23940 no. surface atoms = 1180 nbur = 1853 mkacc time = 0.1700000 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 = 1.456000 m= 279 mr = 3969 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2396 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6306353E-09 -2.8304736E-09 midg,1,midg; midg,igrid,midg -1.9187107E-09 5.2297455E-09 1,midg,midg; igrid,midg,midg 1.0779776E-09 -2.1379083E-09 gauss-seidel spectral radius is 0.9854217 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 14:41:28 rms-change max change #iterations 0.1138484 20.57202 at 10iterations 9.7345272E-03 1.513145 at 20iterations 8.9609058E-04 0.1315498 at 30iterations 1.0086624E-04 1.3080597E-02 at 40iterations 1.5809697E-05 2.2337437E-03 at 50iterations finished qdiffx linear iterations at : 14:41:33 total time elapsed so far: 5.100000 # loops : 50 mean,max change (kT/e) : 1.5809697E-05 2.2337437E-03 energy calculations done at 5.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.290000 DelPhi exited at 14:41:33 5.290u 0.486s 0:06.17 93.5% 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 Sat Oct 8 2011 at 14:41:34 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.785804 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): -14.24100 35.98100 ymin,ymax (A): -14.40800 45.39700 zmin,zma (A): -40.84800 11.77500 x,y,z range (A): 50.22200 59.80500 52.62300 scale (grids/A): 1.785804 object centre (A): 10.87000 15.49450 -14.53650 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 7.1674585E-06 assigned positive charge : 453.7835 centred at (gu) : 94.12057 96.69485 93.30344 assigned negative charge : -453.7843 centred at (gu) : 94.24562 96.43610 93.47981 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23940 grid for indexing accessible points = 1.400000 m= 25270 mr = 55123 m= 2955 mr = 18592 m= 105 mr = 1588 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 29759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 22491 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) : 0.5952679 object centre at (A) : 10.87000 15.49450 -14.53650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8915868E-03 6.1026439E-03 midg,1,midg; midg,igrid,midg -1.9619158E-02 3.8359843E-02 1,midg,midg; igrid,midg,midg 2.6741633E-03 -1.1128355E-02 gauss-seidel spectral radius is 0.9984808 estimated iterations to convergence 203 setup time was (sec) 1.000000 now iterating at: 14:41:35 rms-change max change #iterations 4.057555 175.0482 at 10iterations 1.823098 66.14852 at 20iterations 0.8194526 25.92206 at 30iterations 0.3702695 11.74539 at 40iterations 0.1667996 5.130789 at 50iterations 7.5099811E-02 2.696718 at 60iterations 3.3736769E-02 1.085432 at 70iterations 1.5216090E-02 0.4898834 at 80iterations 6.8661440E-03 0.2175947 at 90iterations 3.0878994E-03 0.1056213 at 100iterations 1.4053384E-03 5.1208496E-02 at 110iterations 6.2943401E-04 1.9737244E-02 at 120iterations finished qdiffx linear iterations at : 14:41:46 total time elapsed so far: 12.26000 # loops : 120 mean,max change (kT/e) : 6.2943401E-04 1.9737244E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 14:41:47 12.436u 0.539s 0:13.30 97.4% 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 Sat Oct 8 2011 at 14:41:47 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.678706 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): -14.24100 35.98100 ymin,ymax (A): -14.40800 45.39700 zmin,zma (A): -40.84800 11.77500 x,y,z range (A): 50.22200 59.80500 52.62300 scale (grids/A): 2.678706 object centre (A): 10.87000 15.49450 -14.53650 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 7.1674585E-06 assigned positive charge : 453.7835 centred at (gu) : 96.18060 100.0423 94.95497 assigned negative charge : -453.7843 centred at (gu) : 96.36838 99.65404 95.21961 start vw surface at 0.1300000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 178388 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23940 grid for indexing accessible points = 1.400000 m= 86688 mr = 134080 m= 26622 mr = 71160 m= 4835 mr = 20872 m= 416 mr = 3428 m= 8 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 67220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 23082 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) : 1.785804 object centre at (A) : 10.87000 15.49450 -14.53650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0075547E-02 0.1982871 midg,1,midg; midg,igrid,midg -0.1830881 0.5813279 1,midg,midg; igrid,midg,midg 5.8908906E-02 -9.0777442E-02 gauss-seidel spectral radius is 0.9992179 estimated iterations to convergence 282 setup time was (sec) 2.040000 now iterating at: 14:41:49 rms-change max change #iterations 9.803979 307.6791 at 10iterations 5.652400 132.2351 at 20iterations 3.235451 70.83479 at 30iterations 1.849944 34.22120 at 40iterations 1.055230 20.85152 at 50iterations 0.5991980 11.74922 at 60iterations 0.3403818 6.177955 at 70iterations 0.1940793 3.457473 at 80iterations 0.1100378 2.041908 at 90iterations 6.2461637E-02 1.161123 at 100iterations 3.5361681E-02 0.6946363 at 110iterations 2.0046582E-02 0.3927879 at 120iterations 1.1370476E-02 0.2075949 at 130iterations 6.4461641E-03 0.1161041 at 140iterations 3.6666240E-03 7.3165894E-02 at 150iterations 2.0797316E-03 3.9482594E-02 at 160iterations 1.1847098E-03 2.1736145E-02 at 170iterations 6.7684380E-04 1.2370110E-02 at 180iterations finished qdiffx linear iterations at : 14:42:08 total time elapsed so far: 20.83000 # loops : 180 mean,max change (kT/e) : 6.7684380E-04 1.2370110E-02 energy calculations done at 20.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.99000 DelPhi exited at 14:42:09 20.991u 0.553s 0:21.83 98.6% 0+0k 0+0io 0pf+0w