Mon Oct 10 14:03:24 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+sph2.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 = amb2.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 14:03:25 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2471 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6658437 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): -78.76400 -27.54500 ymin,ymax (A): 6.660000 60.12600 zmin,zma (A): 59.29800 110.1980 x,y,z range (A): 51.21900 53.46600 50.90000 scale (grids/A): 0.6658437 object centre (A): -53.15450 33.39300 84.74800 number of atom coordinates read : 2471 total number of charged atoms : 2328 net assigned charge : 3.920001 assigned positive charge : 371.5630 centred at (gu) : 87.70825 89.67448 92.12424 assigned negative charge : -367.6435 centred at (gu) : 87.68135 89.66052 91.97536 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7532 nv = 96 ne = 84 npr = 49342 no. pairs analyzed = 49342 no. exposed pairs = 3198 no. arc points = 22657 no. surface atoms = 1068 nbur = 1403 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 477 mr = 4055 m= 6 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2028 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8532 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3685082E-08 6.6395060E-08 midg,1,midg; midg,igrid,midg 8.4653715E-09 1.3074116E-08 1,midg,midg; igrid,midg,midg 7.8891293E-09 1.0584342E-08 gauss-seidel spectral radius is 0.9883021 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 14:03:25 rms-change max change #iterations 0.1691922 23.81570 at 10iterations 1.8731805E-02 2.702999 at 20iterations 2.1266718E-03 0.3203812 at 30iterations 3.7445052E-04 5.0386429E-02 at 40iterations 1.1646139E-04 1.4219284E-02 at 50iterations finished qdiffx linear iterations at : 14:03:28 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.1646139E-04 1.4219284E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 14:03:29 3.501u 0.215s 0:04.45 83.3% 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 Mon Oct 10 2011 at 14:03:29 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2471 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.997531 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): -78.76400 -27.54500 ymin,ymax (A): 6.660000 60.12600 zmin,zma (A): 59.29800 110.1980 x,y,z range (A): 51.21900 53.46600 50.90000 scale (grids/A): 1.997531 object centre (A): -53.15450 33.39300 84.74800 number of atom coordinates read : 2471 total number of charged atoms : 2328 net assigned charge : 3.920001 assigned positive charge : 371.5630 centred at (gu) : 83.12428 89.02294 96.37228 assigned negative charge : -367.6435 centred at (gu) : 83.04388 88.98158 95.92564 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80108 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22657 grid for indexing accessible points = 1.400000 m= 30962 mr = 55024 m= 5612 mr = 22496 m= 419 mr = 3423 m= 9 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 272 time to turn everything in is 0.4100000 number of dielectric boundary points 36001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 18419 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) : 0.6658437 object centre at (A) : -53.15450 33.39300 84.74800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7793823E-02 3.9129905E-02 midg,1,midg; midg,igrid,midg -3.4574836E-02 1.0388419E-02 1,midg,midg; igrid,midg,midg -2.0546953E-03 2.6063347E-02 gauss-seidel spectral radius is 0.9987444 estimated iterations to convergence 224 setup time was (sec) 0.6700000 now iterating at: 14:03:30 rms-change max change #iterations 4.604321 195.3062 at 10iterations 2.227247 73.06484 at 20iterations 1.071943 36.51904 at 30iterations 0.5206658 16.16235 at 40iterations 0.2512521 8.708134 at 50iterations 0.1216123 3.675247 at 60iterations 5.8982141E-02 1.891476 at 70iterations 2.8559355E-02 0.9388046 at 80iterations 1.3798355E-02 0.4633713 at 90iterations 6.7536640E-03 0.2174420 at 100iterations 3.2914185E-03 0.1035633 at 110iterations 1.6268399E-03 4.8280716E-02 at 120iterations finished qdiffx linear iterations at : 14:03:37 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.6268399E-03 4.8280716E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 14:03:39 7.979u 0.246s 0:09.47 86.6% 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 14:03:39 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2471 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.996297 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): -78.76400 -27.54500 ymin,ymax (A): 6.660000 60.12600 zmin,zma (A): 59.29800 110.1980 x,y,z range (A): 51.21900 53.46600 50.90000 scale (grids/A): 2.996297 object centre (A): -53.15450 33.39300 84.74800 number of atom coordinates read : 2471 total number of charged atoms : 2328 net assigned charge : 3.920001 assigned positive charge : 371.5630 centred at (gu) : 79.68629 88.53436 99.55817 assigned negative charge : -367.6435 centred at (gu) : 79.56576 88.47227 98.88838 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 184918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22657 grid for indexing accessible points = 1.400000 m= 96966 mr = 133331 m= 38628 mr = 78746 m= 10283 mr = 30585 m= 1666 mr = 7513 m= 151 mr = 1086 m= 1 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 935 time to turn everything in is 1.090000 number of dielectric boundary points 81268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 18624 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) : 1.997531 object centre at (A) : -53.15450 33.39300 84.74800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2661547 0.2483890 midg,1,midg; midg,igrid,midg -0.9836993 0.1436373 1,midg,midg; igrid,midg,midg -0.1339056 0.2031682 gauss-seidel spectral radius is 0.9992977 estimated iterations to convergence 298 setup time was (sec) 1.330000 now iterating at: 14:03:40 rms-change max change #iterations 10.60183 390.3253 at 10iterations 6.369854 142.9870 at 20iterations 3.796421 83.75668 at 30iterations 2.254927 45.54970 at 40iterations 1.335974 29.29149 at 50iterations 0.7883027 15.59481 at 60iterations 0.4644052 8.379058 at 70iterations 0.2730756 5.323462 at 80iterations 0.1604646 2.933190 at 90iterations 9.4228230E-02 1.791279 at 100iterations 5.5135835E-02 0.9857740 at 110iterations 3.2357685E-02 0.5620651 at 120iterations 1.8914443E-02 0.3264465 at 130iterations 1.1084840E-02 0.2013397 at 140iterations 6.5067294E-03 0.1176071 at 150iterations 3.8421252E-03 6.4670563E-02 at 160iterations 2.2810751E-03 4.3773651E-02 at 170iterations 1.3751541E-03 2.5585175E-02 at 180iterations finished qdiffx linear iterations at : 14:03:52 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 1.3751541E-03 2.5585175E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 14:03:52 12.770u 0.255s 0:13.75 94.6% 0+0k 0+0io 0pf+0w