Sun Oct 9 08:10:13 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 Sun Oct 9 2011 at 08:10:13 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 = 3440 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: 0.5065741 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): -28.94500 41.33100 ymin,ymax (A): -5.793000 48.29900 zmin,zma (A): -15.91400 38.99900 x,y,z range (A): 70.27600 54.09200 54.91300 scale (grids/A): 0.5065741 object centre (A): 6.192999 21.25300 11.54250 number of atom coordinates read : 3440 total number of charged atoms : 3300 net assigned charge : 11.00003 assigned positive charge : 510.6685 centred at (gu) : 88.06837 88.76151 89.42405 assigned negative charge : -499.6699 centred at (gu) : 88.02076 88.81570 89.43761 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5809 nv = 96 ne = 84 npr = 66757 no. pairs analyzed = 66757 no. exposed pairs = 4585 no. arc points = 33566 no. surface atoms = 1531 nbur = 1909 mkacc time = 0.1500000 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 = 1.708000 m= 192 mr = 2768 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3303 ## 528 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7741 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7446096E-10 9.4183258E-11 midg,1,midg; midg,igrid,midg 2.9293545E-10 3.5065666E-11 1,midg,midg; igrid,midg,midg 9.1632292E-11 1.2206613E-10 gauss-seidel spectral radius is 0.9799921 estimated iterations to convergence 58 setup time was (sec) 0.5600000 now iterating at: 08:10:14 rms-change max change #iterations 5.1893365E-02 8.528477 at 10iterations 2.8558716E-03 0.5269594 at 20iterations 1.8414462E-04 2.8276443E-02 at 30iterations 1.9088924E-05 2.5177002E-03 at 40iterations 2.7190881E-06 3.9052963E-04 at 50iterations finished qdiffx linear iterations at : 08:10:17 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 2.7190881E-06 3.9052963E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 08:10:17 3.161u 0.125s 0:03.56 92.1% 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 Sun Oct 9 2011 at 08:10:17 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 = 3440 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: 1.519722 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): -28.94500 41.33100 ymin,ymax (A): -5.793000 48.29900 zmin,zma (A): -15.91400 38.99900 x,y,z range (A): 70.27600 54.09200 54.91300 scale (grids/A): 1.519722 object centre (A): 6.192999 21.25300 11.54250 number of atom coordinates read : 3440 total number of charged atoms : 3300 net assigned charge : 11.00003 assigned positive charge : 510.6685 centred at (gu) : 84.20434 86.28344 88.27142 assigned negative charge : -499.6699 centred at (gu) : 84.06195 86.44673 88.31207 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 64997 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33566 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 17278 mr = 42108 m= 1418 mr = 10914 m= 22 mr = 593 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 30100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 495 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 24712 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) : 0.5065741 object centre at (A) : 6.192999 21.25300 11.54250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7721040E-03 2.7579609E-03 midg,1,midg; midg,igrid,midg 9.6155992E-03 1.5077173E-03 1,midg,midg; igrid,midg,midg -1.4877941E-03 3.0939279E-03 gauss-seidel spectral radius is 0.9979513 estimated iterations to convergence 176 setup time was (sec) 0.7200000 now iterating at: 08:10:18 rms-change max change #iterations 2.990255 141.1199 at 10iterations 1.179253 50.28616 at 20iterations 0.4627367 18.28693 at 30iterations 0.1819475 6.971571 at 40iterations 7.1667336E-02 2.824547 at 50iterations 2.8360434E-02 1.055239 at 60iterations 1.1182318E-02 0.4416771 at 70iterations 4.3971818E-03 0.1589394 at 80iterations 1.7413088E-03 6.9684029E-02 at 90iterations 6.8841758E-04 2.4875641E-02 at 100iterations 2.7254203E-04 9.7217560E-03 at 110iterations 1.0770472E-04 3.8814545E-03 at 120iterations finished qdiffx linear iterations at : 08:10:24 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 1.0770472E-04 3.8814545E-03 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 08:10:24 6.862u 0.163s 0:07.33 95.7% 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 Sun Oct 9 2011 at 08:10:24 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 = 3440 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: 2.279583 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): -28.94500 41.33100 ymin,ymax (A): -5.793000 48.29900 zmin,zma (A): -15.91400 38.99900 x,y,z range (A): 70.27600 54.09200 54.91300 scale (grids/A): 2.279583 object centre (A): 6.192999 21.25300 11.54250 number of atom coordinates read : 3440 total number of charged atoms : 3300 net assigned charge : 11.00003 assigned positive charge : 510.6685 centred at (gu) : 81.30636 84.42500 87.40695 assigned negative charge : -499.6699 centred at (gu) : 81.09290 84.66985 87.46804 start vw surface at 0.1900000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 151532 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33566 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 62496 mr = 104030 m= 14905 mr = 47231 m= 2010 mr = 10461 m= 78 mr = 1218 m= 0 mr = 10 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 68071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 26319 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) : 1.519722 object centre at (A) : 6.192999 21.25300 11.54250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1481636 1.9716825E-02 midg,1,midg; midg,igrid,midg 0.1446957 9.2278025E-04 1,midg,midg; igrid,midg,midg -0.1466238 6.9596484E-02 gauss-seidel spectral radius is 0.9990790 estimated iterations to convergence 260 setup time was (sec) 1.330000 now iterating at: 08:10:26 rms-change max change #iterations 8.251465 270.8867 at 10iterations 4.639966 123.0644 at 20iterations 2.564081 65.83256 at 30iterations 1.411535 38.30964 at 40iterations 0.7722893 18.44180 at 50iterations 0.4203726 10.19990 at 60iterations 0.2280865 5.633488 at 70iterations 0.1237959 2.713132 at 80iterations 6.6896990E-02 1.415611 at 90iterations 3.6222558E-02 1.096094 at 100iterations 1.9537902E-02 0.3978577 at 110iterations 1.0548120E-02 0.2145119 at 120iterations 5.6795068E-03 0.1191082 at 130iterations 3.0666622E-03 6.3154221E-02 at 140iterations 1.6516660E-03 3.7183762E-02 at 150iterations 8.8986428E-04 1.7606974E-02 at 160iterations 4.7935848E-04 9.5996857E-03 at 170iterations 2.5842717E-04 5.0821304E-03 at 180iterations finished qdiffx linear iterations at : 08:10:35 total time elapsed so far: 10.88000 # loops : 180 mean,max change (kT/e) : 2.5842717E-04 5.0821304E-03 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 08:10:36 11.063u 0.174s 0:11.58 96.9% 0+0k 0+0io 0pf+0w