Tue Nov 22 14:14:16 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+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 Tue Nov 22 2011 at 14:14:20 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2130 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: 0.6480150 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): -5.352000 33.35100 ymin,ymax (A): -3.299000 46.68600 zmin,zma (A): -8.018001 46.91900 x,y,z range (A): 38.70300 49.98500 54.93700 scale (grids/A): 0.6480150 object centre (A): 13.99950 21.69350 19.45050 number of atom coordinates read : 2130 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 290.5620 centred at (gu) : 89.71061 92.88358 89.86861 assigned negative charge : -285.5623 centred at (gu) : 89.64371 92.97651 89.91718 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5580 nv = 96 ne = 84 npr = 40749 no. pairs analyzed = 40749 no. exposed pairs = 2455 no. arc points = 17231 no. surface atoms = 834 nbur = 1296 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 263 mr = 3096 m= 0 mr = 32 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.1700000 number of dielectric boundary points 2715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1670 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6495 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4891850E-08 4.1449923E-09 midg,1,midg; midg,igrid,midg 1.0526453E-08 -1.5390079E-09 1,midg,midg; igrid,midg,midg 2.4085531E-09 1.5435138E-08 gauss-seidel spectral radius is 0.9876017 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 14:14:24 rms-change max change #iterations 0.1333494 24.33206 at 10iterations 1.3172387E-02 1.963009 at 20iterations 1.3683680E-03 0.2098808 at 30iterations 1.3850322E-04 2.3895264E-02 at 40iterations 1.3843111E-05 2.0685196E-03 at 50iterations finished qdiffx linear iterations at : 14:14:33 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 1.3843111E-05 2.0685196E-03 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 14:14:35 3.776u 0.221s 0:15.10 26.4% 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 Tue Nov 22 2011 at 14:14:41 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2130 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: 1.944045 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): -5.352000 33.35100 ymin,ymax (A): -3.299000 46.68600 zmin,zma (A): -8.018001 46.91900 x,y,z range (A): 38.70300 49.98500 54.93700 scale (grids/A): 1.944045 object centre (A): 13.99950 21.69350 19.45050 number of atom coordinates read : 2130 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 290.5620 centred at (gu) : 89.13217 98.65086 89.60560 assigned negative charge : -285.5623 centred at (gu) : 88.93120 98.92976 89.75154 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 60119 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17231 grid for indexing accessible points = 1.400000 m= 20910 mr = 41390 m= 2868 mr = 15814 m= 154 mr = 1734 m= 0 mr = 48 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 633 time to turn everything in is 0.3300000 number of dielectric boundary points 25065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14324 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) : 0.6480150 object centre at (A) : 13.99950 21.69350 19.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3047277E-02 4.6110351E-02 midg,1,midg; midg,igrid,midg 2.7199009E-02 -5.0529563E-03 1,midg,midg; igrid,midg,midg 8.1908256E-03 5.9218272E-03 gauss-seidel spectral radius is 0.9986079 estimated iterations to convergence 212 setup time was (sec) 0.5600000 now iterating at: 14:14:46 rms-change max change #iterations 3.717955 168.8817 at 10iterations 1.723804 64.90944 at 20iterations 0.8019106 28.82566 at 30iterations 0.3728866 14.58077 at 40iterations 0.1723296 6.154438 at 50iterations 8.0199338E-02 2.794452 at 60iterations 3.7404571E-02 1.318995 at 70iterations 1.7336510E-02 0.5991402 at 80iterations 8.0473870E-03 0.2743034 at 90iterations 3.7311739E-03 0.1279612 at 100iterations 1.7415409E-03 5.7372570E-02 at 110iterations 8.0872234E-04 2.5482178E-02 at 120iterations finished qdiffx linear iterations at : 14:15:09 total time elapsed so far: 8.440000 # loops : 120 mean,max change (kT/e) : 8.0872234E-04 2.5482178E-02 energy calculations done at 8.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.560000 DelPhi exited at 14:15:11 8.566u 0.252s 0:30.40 28.9% 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 Nov 22 2011 at 14:15:12 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2130 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: 2.916067 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): -5.352000 33.35100 ymin,ymax (A): -3.299000 46.68600 zmin,zma (A): -8.018001 46.91900 x,y,z range (A): 38.70300 49.98500 54.93700 scale (grids/A): 2.916067 object centre (A): 13.99950 21.69350 19.45050 number of atom coordinates read : 2130 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 290.5620 centred at (gu) : 88.69811 102.9763 89.40836 assigned negative charge : -285.5623 centred at (gu) : 88.39687 103.3947 89.62737 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 139104 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17231 grid for indexing accessible points = 1.400000 m= 69213 mr = 100482 m= 23637 mr = 57251 m= 4958 mr = 19216 m= 599 mr = 3707 m= 25 mr = 363 m= 0 mr = 7 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2089 time to turn everything in is 0.8000000 number of dielectric boundary points 56510 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14604 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) : 1.944045 object centre at (A) : 13.99950 21.69350 19.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6658504E-02 1.074373 midg,1,midg; midg,igrid,midg 0.2713101 -6.9492668E-02 1,midg,midg; igrid,midg,midg 0.1063666 2.9599231E-02 gauss-seidel spectral radius is 0.9992390 estimated iterations to convergence 286 setup time was (sec) 1.060000 now iterating at: 14:15:19 rms-change max change #iterations 8.725591 439.8673 at 10iterations 5.024290 128.7324 at 20iterations 2.877852 69.23045 at 30iterations 1.641769 39.01997 at 40iterations 0.9376895 21.23004 at 50iterations 0.5367206 11.21794 at 60iterations 0.3051073 6.147121 at 70iterations 0.1740183 3.464580 at 80iterations 9.9093363E-02 1.942703 at 90iterations 5.6468345E-02 1.311819 at 100iterations 3.2091115E-02 0.7149005 at 110iterations 1.8287962E-02 0.3381157 at 120iterations 1.0412539E-02 0.2346153 at 130iterations 5.9330063E-03 0.1134591 at 140iterations 3.3697232E-03 6.7534983E-02 at 150iterations 1.9142475E-03 3.7701607E-02 at 160iterations 1.0904410E-03 2.2247314E-02 at 170iterations 6.2060455E-04 1.1928558E-02 at 180iterations finished qdiffx linear iterations at : 14:15:57 total time elapsed so far: 13.75000 # loops : 180 mean,max change (kT/e) : 6.2060455E-04 1.1928558E-02 energy calculations done at 13.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.89000 DelPhi exited at 14:15:58 13.887u 0.240s 0:46.20 30.5% 0+0k 0+0io 0pf+0w