Wed Dec 28 11:01:04 PST 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 Wed Dec 28 2011 at 11:01:04 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5876235 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): -35.22000 10.09900 ymin,ymax (A): 0.9390000 40.93000 zmin,zma (A): -2.192000 58.39100 x,y,z range (A): 45.31900 39.99100 60.58300 scale (grids/A): 0.5876235 object centre (A): -12.56050 20.93450 28.09950 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681006 assigned positive charge : 287.8141 centred at (gu) : 90.45259 89.73276 89.77022 assigned negative charge : -285.1333 centred at (gu) : 90.34913 89.86880 89.75178 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4542 nv = 96 ne = 84 npr = 40416 no. pairs analyzed = 40416 no. exposed pairs = 2384 no. arc points = 17088 no. surface atoms = 804 nbur = 1161 mkacc time = 7.0000008E-02 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= 191 mr = 2489 m= 0 mr = 15 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1752 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5646 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3401677E-10 1.0269774E-09 midg,1,midg; midg,igrid,midg 3.3804619E-09 -1.6492649E-09 1,midg,midg; igrid,midg,midg -1.0311839E-09 2.8910505E-09 gauss-seidel spectral radius is 0.9849644 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 11:01:05 rms-change max change #iterations 8.1667401E-02 15.65911 at 10iterations 6.6177989E-03 1.284168 at 20iterations 5.2744668E-04 0.1203289 at 30iterations 4.2498705E-05 8.2244873E-03 at 40iterations 3.3719743E-06 5.8341026E-04 at 50iterations finished qdiffx linear iterations at : 11:01:08 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 3.3719743E-06 5.8341026E-04 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 11:01:09 3.773u 0.267s 0:04.59 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 Wed Dec 28 2011 at 11:01:09 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.762871 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): -35.22000 10.09900 ymin,ymax (A): 0.9390000 40.93000 zmin,zma (A): -2.192000 58.39100 x,y,z range (A): 45.31900 39.99100 60.58300 scale (grids/A): 1.762871 object centre (A): -12.56050 20.93450 28.09950 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681006 assigned positive charge : 287.8141 centred at (gu) : 91.35799 89.19797 89.31043 assigned negative charge : -285.1333 centred at (gu) : 91.04755 89.60637 89.25538 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 49277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17088 grid for indexing accessible points = 1.400000 m= 17099 mr = 33758 m= 2154 mr = 12882 m= 84 mr = 1304 m= 0 mr = 21 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 797 time to turn everything in is 0.2700000 number of dielectric boundary points 20649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 214 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 14283 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) : 0.5876235 object centre at (A) : -12.56050 20.93450 28.09950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6128953E-02 2.1201782E-02 midg,1,midg; midg,igrid,midg 1.2703525E-03 -7.6910066E-03 1,midg,midg; igrid,midg,midg -3.0545781E-03 9.8607817E-04 gauss-seidel spectral radius is 0.9983298 estimated iterations to convergence 194 setup time was (sec) 0.5600000 now iterating at: 11:01:10 rms-change max change #iterations 3.052578 151.5214 at 10iterations 1.315928 62.86465 at 20iterations 0.5672432 22.14849 at 30iterations 0.2448453 9.627918 at 40iterations 0.1058616 4.252960 at 50iterations 4.5807634E-02 1.694170 at 60iterations 1.9764014E-02 0.7388916 at 70iterations 8.5164467E-03 0.3391609 at 80iterations 3.6695572E-03 0.1477280 at 90iterations 1.5920602E-03 6.0717106E-02 at 100iterations 6.8809045E-04 2.6893616E-02 at 110iterations 2.9802200E-04 1.3320923E-02 at 120iterations finished qdiffx linear iterations at : 11:01:19 total time elapsed so far: 9.990000 # loops : 120 mean,max change (kT/e) : 2.9802200E-04 1.3320923E-02 energy calculations done at 9.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 11:01:21 10.122u 0.350s 0:12.13 86.3% 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 Wed Dec 28 2011 at 11:01:21 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.644306 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): -35.22000 10.09900 ymin,ymax (A): 0.9390000 40.93000 zmin,zma (A): -2.192000 58.39100 x,y,z range (A): 45.31900 39.99100 60.58300 scale (grids/A): 2.644306 object centre (A): -12.56050 20.93450 28.09950 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681006 assigned positive charge : 287.8141 centred at (gu) : 92.03701 88.79699 88.96566 assigned negative charge : -285.1333 centred at (gu) : 91.57129 89.40960 88.88309 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 113893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17088 grid for indexing accessible points = 1.400000 m= 56847 mr = 81582 m= 19089 mr = 47116 m= 3591 mr = 15632 m= 325 mr = 2663 m= 6 mr = 223 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2666 time to turn everything in is 0.7800000 number of dielectric boundary points 46535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 14651 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) : 1.762871 object centre at (A) : -12.56050 20.93450 28.09950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3221326 0.1547982 midg,1,midg; midg,igrid,midg -9.8129641E-03 -0.1079989 1,midg,midg; igrid,midg,midg -5.6006044E-02 -2.6289010E-02 gauss-seidel spectral radius is 0.9991496 estimated iterations to convergence 271 setup time was (sec) 1.190000 now iterating at: 11:01:23 rms-change max change #iterations 7.393530 257.3070 at 10iterations 4.098740 112.1330 at 20iterations 2.276612 57.04101 at 30iterations 1.256007 27.88367 at 40iterations 0.6899309 16.91481 at 50iterations 0.3797023 8.559133 at 60iterations 0.2089019 4.944651 at 70iterations 0.1147203 2.871989 at 80iterations 6.3170105E-02 1.560200 at 90iterations 3.4843102E-02 0.7360020 at 100iterations 1.9126665E-02 0.4320803 at 110iterations 1.0530652E-02 0.2619238 at 120iterations 5.7853754E-03 0.1274086 at 130iterations 3.1874501E-03 7.3391914E-02 at 140iterations 1.7550350E-03 3.9299011E-02 at 150iterations 9.6441613E-04 2.2911072E-02 at 160iterations 5.3220754E-04 1.1680603E-02 at 170iterations 2.9298349E-04 6.7863464E-03 at 180iterations finished qdiffx linear iterations at : 11:01:40 total time elapsed so far: 18.07000 # loops : 180 mean,max change (kT/e) : 2.9298349E-04 6.7863464E-03 energy calculations done at 18.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.21000 DelPhi exited at 11:01:40 18.212u 0.549s 0:19.11 98.1% 0+0k 0+0io 0pf+0w