Mon Oct 10 14:09:05 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 Mon Oct 10 2011 at 14:09:05 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2614 !!! WARNING: MG3 365 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5774814 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): 23.21000 79.97200 ymin,ymax (A): -10.56500 51.08200 zmin,zma (A): 2.807000 54.69000 x,y,z range (A): 56.76200 61.64700 51.88300 scale (grids/A): 0.5774814 object centre (A): 51.59100 20.25850 28.74850 number of atom coordinates read : 2614 total number of charged atoms : 2479 net assigned charge : -1.599989 assigned positive charge : 379.5668 centred at (gu) : 89.09732 88.42750 89.90786 assigned negative charge : -381.1673 centred at (gu) : 89.01488 88.46584 89.84435 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5801 nv = 96 ne = 84 npr = 53482 no. pairs analyzed = 53482 no. exposed pairs = 3302 no. arc points = 23969 no. surface atoms = 1116 nbur = 1498 mkacc time = 0.1200000 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 = 1.484000 m= 278 mr = 2983 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3200000 number of dielectric boundary points 3088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2386 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7298 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4524185E-09 7.5891493E-10 midg,1,midg; midg,igrid,midg 5.1497928E-10 -6.7929062E-10 1,midg,midg; igrid,midg,midg -2.1759576E-09 8.8303553E-10 gauss-seidel spectral radius is 0.9844981 estimated iterations to convergence 66 setup time was (sec) 0.5500000 now iterating at: 14:09:06 rms-change max change #iterations 8.8362351E-02 15.16296 at 10iterations 6.8012229E-03 0.9791603 at 20iterations 5.2002812E-04 8.2328796E-02 at 30iterations 4.1375733E-05 6.8168640E-03 at 40iterations 3.1166353E-06 5.4740906E-04 at 50iterations finished qdiffx linear iterations at : 14:09:08 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.1166353E-06 5.4740906E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:09:09 3.432u 0.155s 0:03.90 91.7% 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 Mon Oct 10 2011 at 14:09:09 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2614 !!! WARNING: MG3 365 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.732444 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): 23.21000 79.97200 ymin,ymax (A): -10.56500 51.08200 zmin,zma (A): 2.807000 54.69000 x,y,z range (A): 56.76200 61.64700 51.88300 scale (grids/A): 1.732444 object centre (A): 51.59100 20.25850 28.74850 number of atom coordinates read : 2614 total number of charged atoms : 2479 net assigned charge : -1.599989 assigned positive charge : 379.5668 centred at (gu) : 87.29134 85.28196 89.72307 assigned negative charge : -381.1673 centred at (gu) : 87.04436 85.39731 89.53281 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 63390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23969 grid for indexing accessible points = 1.400000 m= 20100 mr = 42264 m= 2324 mr = 13841 m= 91 mr = 1270 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1951 time to turn everything in is 0.5100000 number of dielectric boundary points 28518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19226 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) : 0.5774814 object centre at (A) : 51.59100 20.25850 28.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1632912E-02 1.3921005E-03 midg,1,midg; midg,igrid,midg 8.1339041E-03 -5.4232130E-04 1,midg,midg; igrid,midg,midg -3.0843189E-02 6.8215327E-03 gauss-seidel spectral radius is 0.9983495 estimated iterations to convergence 195 setup time was (sec) 0.8300000 now iterating at: 14:09:10 rms-change max change #iterations 3.451682 178.7628 at 10iterations 1.495302 53.91894 at 20iterations 0.6486859 23.95046 at 30iterations 0.2807501 11.08273 at 40iterations 0.1216469 4.354064 at 50iterations 5.2682787E-02 1.921710 at 60iterations 2.2843016E-02 0.8381376 at 70iterations 9.9117095E-03 0.3875160 at 80iterations 4.2927302E-03 0.1503220 at 90iterations 1.8642282E-03 6.8105698E-02 at 100iterations 8.0947852E-04 2.9972076E-02 at 110iterations 3.5071763E-04 1.2451172E-02 at 120iterations finished qdiffx linear iterations at : 14:09:17 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 3.5071763E-04 1.2451172E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 14:09:18 8.142u 0.270s 0:08.76 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 Mon Oct 10 2011 at 14:09:18 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2614 !!! WARNING: MG3 365 has a net charge of 1.4000 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: 2.598667 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): 23.21000 79.97200 ymin,ymax (A): -10.56500 51.08200 zmin,zma (A): 2.807000 54.69000 x,y,z range (A): 56.76200 61.64700 51.88300 scale (grids/A): 2.598667 object centre (A): 51.59100 20.25850 28.74850 number of atom coordinates read : 2614 total number of charged atoms : 2479 net assigned charge : -1.599989 assigned positive charge : 379.5668 centred at (gu) : 85.93688 82.92279 89.58452 assigned negative charge : -381.1673 centred at (gu) : 85.56644 83.09584 89.29909 start vw surface at 0.1900000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 146926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23969 grid for indexing accessible points = 1.400000 m= 68049 mr = 103248 m= 20795 mr = 53894 m= 3920 mr = 15781 m= 388 mr = 2739 m= 11 mr = 192 m= 0 mr = 1 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 6536 time to turn everything in is 1.260000 number of dielectric boundary points 64234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 19825 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) : 1.732444 object centre at (A) : 51.59100 20.25850 28.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2125521 1.1325396E-02 midg,1,midg; midg,igrid,midg 0.1412369 -0.1340867 1,midg,midg; igrid,midg,midg -0.4876700 8.4626324E-02 gauss-seidel spectral radius is 0.9991772 estimated iterations to convergence 275 setup time was (sec) 1.600000 now iterating at: 14:09:20 rms-change max change #iterations 8.596611 271.3025 at 10iterations 4.856842 124.2875 at 20iterations 2.720330 59.96615 at 30iterations 1.524209 41.30618 at 40iterations 0.8497217 18.44694 at 50iterations 0.4738048 9.147028 at 60iterations 0.2647929 6.580822 at 70iterations 0.1472906 3.222139 at 80iterations 8.1843220E-02 1.786232 at 90iterations 4.5460112E-02 0.9346962 at 100iterations 2.5304254E-02 0.4781342 at 110iterations 1.4055897E-02 0.3005991 at 120iterations 7.8151301E-03 0.1482668 at 130iterations 4.3491577E-03 8.4995329E-02 at 140iterations 2.4150182E-03 4.9079895E-02 at 150iterations 1.3419830E-03 2.7821064E-02 at 160iterations 7.4711232E-04 1.3862610E-02 at 170iterations 4.1572854E-04 8.9035034E-03 at 180iterations finished qdiffx linear iterations at : 14:09:31 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 4.1572854E-04 8.9035034E-03 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 14:09:32 13.345u 0.289s 0:13.95 97.6% 0+0k 0+0io 0pf+0w