Wed Dec 21 14:23:02 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 Wed Dec 21 2011 at 14:23:05 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6021447 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): -24.12500 34.99700 ymin,ymax (A): -19.71600 20.26100 zmin,zma (A): -2.818000 38.66700 x,y,z range (A): 59.12200 39.97700 41.48500 scale (grids/A): 0.6021447 object centre (A): 5.436001 0.2725000 17.92450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.4260 centred at (gu) : 89.73403 90.55508 90.21008 assigned negative charge : -289.4262 centred at (gu) : 89.73438 90.65942 90.36842 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4813 nv = 96 ne = 84 npr = 40223 no. pairs analyzed = 40223 no. exposed pairs = 2403 no. arc points = 16976 no. surface atoms = 816 nbur = 1148 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 195 mr = 2649 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.3000000 number of dielectric boundary points 2341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1808 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 5923 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2190563E-09 -3.9232808E-09 midg,1,midg; midg,igrid,midg 3.4839038E-09 -2.4134266E-09 1,midg,midg; igrid,midg,midg 1.0223762E-09 8.9063312E-10 gauss-seidel spectral radius is 0.9856713 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 14:23:06 rms-change max change #iterations 0.1000789 16.52040 at 10iterations 8.2794987E-03 1.511424 at 20iterations 7.0791255E-04 0.1224365 at 30iterations 6.0908307E-05 1.0110855E-02 at 40iterations 5.2077548E-06 8.3708763E-04 at 50iterations finished qdiffx linear iterations at : 14:23:10 total time elapsed so far: 4.630000 # loops : 50 mean,max change (kT/e) : 5.2077548E-06 8.3708763E-04 energy calculations done at 4.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.850000 DelPhi exited at 14:23:12 4.858u 0.481s 0:07.06 75.4% 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 Wed Dec 21 2011 at 14:23:12 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.806434 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): -24.12500 34.99700 ymin,ymax (A): -19.71600 20.26100 zmin,zma (A): -2.818000 38.66700 x,y,z range (A): 59.12200 39.97700 41.48500 scale (grids/A): 1.806434 object centre (A): 5.436001 0.2725000 17.92450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.4260 centred at (gu) : 89.20216 91.66542 90.63021 assigned negative charge : -289.4262 centred at (gu) : 89.20335 91.97855 91.10527 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 52238 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 18322 mr = 36023 m= 2358 mr = 13931 m= 74 mr = 1489 m= 0 mr = 16 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1032 time to turn everything in is 0.5800000 number of dielectric boundary points 21533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14322 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) : 0.6021447 object centre at (A) : 5.436001 0.2725000 17.92450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7721394E-03 -9.8599996E-03 midg,1,midg; midg,igrid,midg 5.4099159E-03 -4.5010210E-03 1,midg,midg; igrid,midg,midg 4.2002529E-02 2.9124975E-02 gauss-seidel spectral radius is 0.9984053 estimated iterations to convergence 199 setup time was (sec) 1.100000 now iterating at: 14:23:14 rms-change max change #iterations 3.269538 168.6183 at 10iterations 1.440348 59.93754 at 20iterations 0.6341001 24.27136 at 30iterations 0.2779894 10.97888 at 40iterations 0.1225975 4.823551 at 50iterations 5.3998206E-02 1.986837 at 60iterations 2.3838470E-02 0.9236321 at 70iterations 1.0470849E-02 0.4066696 at 80iterations 4.6299733E-03 0.1768265 at 90iterations 2.0273651E-03 7.6909542E-02 at 100iterations 8.9576212E-04 3.6193132E-02 at 110iterations 3.9577647E-04 1.5981197E-02 at 120iterations finished qdiffx linear iterations at : 14:23:28 total time elapsed so far: 15.56000 # loops : 120 mean,max change (kT/e) : 3.9577647E-04 1.5981197E-02 energy calculations done at 15.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.79000 DelPhi exited at 14:23:29 15.794u 0.690s 0:16.97 97.1% 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 Wed Dec 21 2011 at 14:23:29 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.709651 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): -24.12500 34.99700 ymin,ymax (A): -19.71600 20.26100 zmin,zma (A): -2.818000 38.66700 x,y,z range (A): 59.12200 39.97700 41.48500 scale (grids/A): 2.709651 object centre (A): 5.436001 0.2725000 17.92450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.4260 centred at (gu) : 88.80317 92.49794 90.94528 assigned negative charge : -289.4262 centred at (gu) : 88.80516 92.96788 91.65800 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 120738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 60419 mr = 87044 m= 20518 mr = 50320 m= 4129 mr = 16931 m= 350 mr = 3189 m= 5 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 3421 time to turn everything in is 1.500000 number of dielectric boundary points 48494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 14655 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) : 1.806434 object centre at (A) : 5.436001 0.2725000 17.92450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7270290E-02 -9.8935649E-02 midg,1,midg; midg,igrid,midg 4.6710826E-02 -3.9517224E-02 1,midg,midg; igrid,midg,midg 0.4638535 0.3053473 gauss-seidel spectral radius is 0.9991737 estimated iterations to convergence 275 setup time was (sec) 2.000000 now iterating at: 14:23:32 rms-change max change #iterations 7.806262 290.3815 at 10iterations 4.372929 118.7723 at 20iterations 2.444122 60.48647 at 30iterations 1.353033 31.72869 at 40iterations 0.7528746 16.18154 at 50iterations 0.4173976 9.219711 at 60iterations 0.2322941 5.161022 at 70iterations 0.1289892 3.292722 at 80iterations 7.1371883E-02 1.565283 at 90iterations 3.9627213E-02 0.9442592 at 100iterations 2.1967556E-02 0.5005226 at 110iterations 1.2215614E-02 0.2592273 at 120iterations 6.7816102E-03 0.1548476 at 130iterations 3.7645020E-03 8.0840111E-02 at 140iterations 2.0866278E-03 5.0598145E-02 at 150iterations 1.1616069E-03 2.4791718E-02 at 160iterations 6.4330961E-04 1.4177322E-02 at 170iterations 3.5784289E-04 7.6794624E-03 at 180iterations finished qdiffx linear iterations at : 14:23:56 total time elapsed so far: 26.09000 # loops : 180 mean,max change (kT/e) : 3.5784289E-04 7.6794624E-03 energy calculations done at 26.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 26.31000 DelPhi exited at 14:23:57 26.319u 0.763s 0:27.48 98.5% 0+0k 0+0io 0pf+0w