Sat Oct 8 21:57:02 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 Sat Oct 8 2011 at 21:57:02 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: GLM 128 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6723832 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): -6.695000 44.04600 ymin,ymax (A): -26.78500 26.16100 zmin,zma (A): 3.113000 54.24000 x,y,z range (A): 50.74100 52.94600 51.12700 scale (grids/A): 0.6723832 object centre (A): 18.67550 -0.3119993 28.67650 number of atom coordinates read : 2517 total number of charged atoms : 2399 net assigned charge : 3.920002 assigned positive charge : 381.8789 centred at (gu) : 88.20318 89.55894 92.02579 assigned negative charge : -377.9593 centred at (gu) : 88.23123 89.52280 91.92094 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8023 nv = 96 ne = 84 npr = 48876 no. pairs analyzed = 48876 no. exposed pairs = 3294 no. arc points = 23409 no. surface atoms = 1102 nbur = 1415 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 511 mr = 4402 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2157 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4247090E-09 6.1055530E-08 midg,1,midg; midg,igrid,midg 3.8251979E-09 2.0529789E-08 1,midg,midg; igrid,midg,midg 2.9290810E-08 4.1233137E-09 gauss-seidel spectral radius is 0.9885331 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 21:57:03 rms-change max change #iterations 0.1863950 28.09715 at 10iterations 2.0340601E-02 2.455688 at 20iterations 2.2565864E-03 0.3703842 at 30iterations 3.0476911E-04 4.4788361E-02 at 40iterations 7.5765864E-05 1.1777878E-02 at 50iterations finished qdiffx linear iterations at : 21:57:05 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 7.5765864E-05 1.1777878E-02 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 21:57:06 3.143u 0.171s 0:03.59 92.2% 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 21:57:06 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: GLM 128 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.017150 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): -6.695000 44.04600 ymin,ymax (A): -26.78500 26.16100 zmin,zma (A): 3.113000 54.24000 x,y,z range (A): 50.74100 52.94600 51.12700 scale (grids/A): 2.017150 object centre (A): 18.67550 -0.3119993 28.67650 number of atom coordinates read : 2517 total number of charged atoms : 2399 net assigned charge : 3.920002 assigned positive charge : 381.8789 centred at (gu) : 84.60895 88.67618 96.07680 assigned negative charge : -377.9593 centred at (gu) : 84.69331 88.56801 95.76237 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 84690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23409 grid for indexing accessible points = 1.400000 m= 32359 mr = 58687 m= 6045 mr = 23624 m= 511 mr = 3837 m= 10 mr = 211 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 171 time to turn everything in is 0.5900000 number of dielectric boundary points 37256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 18953 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) : 0.6723832 object centre at (A) : 18.67550 -0.3119993 28.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9301526E-02 3.9061576E-02 midg,1,midg; midg,igrid,midg -2.9490132E-02 -1.7140724E-02 1,midg,midg; igrid,midg,midg 4.6492796E-02 2.1884950E-02 gauss-seidel spectral radius is 0.9987771 estimated iterations to convergence 226 setup time was (sec) 0.8700000 now iterating at: 21:57:07 rms-change max change #iterations 4.742352 196.9953 at 10iterations 2.319706 70.31560 at 20iterations 1.132562 35.00556 at 30iterations 0.5542831 16.34919 at 40iterations 0.2716234 8.191458 at 50iterations 0.1328635 3.711493 at 60iterations 6.4809427E-02 1.862549 at 70iterations 3.1502262E-02 0.8831596 at 80iterations 1.5398310E-02 0.4481001 at 90iterations 7.5691259E-03 0.2177391 at 100iterations 3.6897794E-03 0.1083298 at 110iterations 1.8075302E-03 5.2643776E-02 at 120iterations finished qdiffx linear iterations at : 21:57:13 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 1.8075302E-03 5.2643776E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 21:57:13 7.188u 0.215s 0:07.69 96.0% 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 21:57:13 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: GLM 128 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.025724 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): -6.695000 44.04600 ymin,ymax (A): -26.78500 26.16100 zmin,zma (A): 3.113000 54.24000 x,y,z range (A): 50.74100 52.94600 51.12700 scale (grids/A): 3.025724 object centre (A): 18.67550 -0.3119993 28.67650 number of atom coordinates read : 2517 total number of charged atoms : 2399 net assigned charge : 3.920002 assigned positive charge : 381.8789 centred at (gu) : 81.91338 88.01427 99.11514 assigned negative charge : -377.9593 centred at (gu) : 82.03980 87.85188 98.64365 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 195409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23409 grid for indexing accessible points = 1.400000 m= 102083 mr = 141775 m= 39671 mr = 83402 m= 11337 mr = 31549 m= 2192 mr = 8461 m= 156 mr = 1585 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 574 time to turn everything in is 1.550000 number of dielectric boundary points 83994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 19192 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) : 2.017150 object centre at (A) : 18.67550 -0.3119993 28.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4481055 0.3194018 midg,1,midg; midg,igrid,midg -0.6308547 -0.3255565 1,midg,midg; igrid,midg,midg 0.4550093 0.1058950 gauss-seidel spectral radius is 0.9993113 estimated iterations to convergence 301 setup time was (sec) 1.860000 now iterating at: 21:57:15 rms-change max change #iterations 10.95745 335.1619 at 10iterations 6.622234 148.2910 at 20iterations 3.963868 83.32257 at 30iterations 2.362364 49.48849 at 40iterations 1.402246 25.54662 at 50iterations 0.8355430 16.08951 at 60iterations 0.4941111 8.904917 at 70iterations 0.2913246 5.535219 at 80iterations 0.1718657 3.465500 at 90iterations 0.1014974 1.699760 at 100iterations 5.9719291E-02 1.047012 at 110iterations 3.5131678E-02 0.5668068 at 120iterations 2.0630099E-02 0.3763540 at 130iterations 1.2136435E-02 0.2284851 at 140iterations 7.1378532E-03 0.1170891 at 150iterations 4.2034732E-03 6.8371773E-02 at 160iterations 2.4772144E-03 4.1584015E-02 at 170iterations 1.4649063E-03 2.3602486E-02 at 180iterations finished qdiffx linear iterations at : 21:57:25 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 1.4649063E-03 2.3602486E-02 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 21:57:26 12.066u 0.212s 0:12.61 97.3% 0+0k 0+0io 0pf+0w