Sat Oct 8 20:05:03 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 20:05:03 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 657 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6168882 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): -32.16200 17.54800 ymin,ymax (A): -24.45600 23.14900 zmin,zma (A): -12.39600 45.31300 x,y,z range (A): 49.71000 47.60500 57.70900 scale (grids/A): 0.6168882 object centre (A): -7.306999 -0.6534996 16.45850 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 88.76582 89.31951 89.50649 assigned negative charge : -393.5505 centred at (gu) : 88.66988 89.37271 89.41682 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 54973 no. pairs analyzed = 54973 no. exposed pairs = 3078 no. arc points = 22122 no. surface atoms = 1030 nbur = 1589 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 3527 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.1900000 number of dielectric boundary points 3169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2247 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2749243E-09 7.2635196E-09 midg,1,midg; midg,igrid,midg 6.8558519E-09 -5.2929500E-10 1,midg,midg; igrid,midg,midg -4.4295323E-09 6.4602999E-09 gauss-seidel spectral radius is 0.9863896 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 20:05:03 rms-change max change #iterations 0.1252787 19.42270 at 10iterations 1.1318348E-02 1.651043 at 20iterations 1.0260267E-03 0.1670074 at 30iterations 9.4156341E-05 1.3489962E-02 at 40iterations 8.5182537E-06 1.2760162E-03 at 50iterations finished qdiffx linear iterations at : 20:05:07 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 8.5182537E-06 1.2760162E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 20:05:07 3.440u 0.195s 0:04.69 77.3% 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 20:05:07 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 657 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.850664 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): -32.16200 17.54800 ymin,ymax (A): -24.45600 23.14900 zmin,zma (A): -12.39600 45.31300 x,y,z range (A): 49.71000 47.60500 57.70900 scale (grids/A): 1.850664 object centre (A): -7.306999 -0.6534996 16.45850 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 86.29732 87.95792 88.51890 assigned negative charge : -393.5505 centred at (gu) : 86.00943 88.11789 88.25037 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22122 grid for indexing accessible points = 1.400000 m= 23266 mr = 48939 m= 3072 mr = 16832 m= 138 mr = 1832 m= 3 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5689 time to turn everything in is 0.3300000 number of dielectric boundary points 29234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19405 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) : 0.6168882 object centre at (A) : -7.306999 -0.6534996 16.45850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1613065E-02 1.9699406E-02 midg,1,midg; midg,igrid,midg 1.0682722E-02 -1.9903227E-03 1,midg,midg; igrid,midg,midg -3.0346436E-03 2.6240781E-02 gauss-seidel spectral radius is 0.9985566 estimated iterations to convergence 209 setup time was (sec) 0.5500000 now iterating at: 20:05:08 rms-change max change #iterations 4.054287 168.9083 at 10iterations 1.857380 60.94546 at 20iterations 0.8516321 30.07497 at 30iterations 0.3906923 13.54229 at 40iterations 0.1789669 5.706085 at 50iterations 8.2080960E-02 2.708536 at 60iterations 3.7611548E-02 1.191256 at 70iterations 1.7214378E-02 0.5665665 at 80iterations 7.8979153E-03 0.2530861 at 90iterations 3.6319958E-03 0.1178780 at 100iterations 1.6669551E-03 5.3825378E-02 at 110iterations 7.6187216E-04 2.4872303E-02 at 120iterations finished qdiffx linear iterations at : 20:05:15 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 7.6187216E-04 2.4872303E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 20:05:16 7.756u 0.222s 0:08.30 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 20:05:16 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 657 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.775997 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): -32.16200 17.54800 ymin,ymax (A): -24.45600 23.14900 zmin,zma (A): -12.39600 45.31300 x,y,z range (A): 49.71000 47.60500 57.70900 scale (grids/A): 2.775997 object centre (A): -7.306999 -0.6534996 16.45850 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 84.44571 86.93679 87.77825 assigned negative charge : -393.5505 centred at (gu) : 84.01405 87.17678 87.37539 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 163146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22122 grid for indexing accessible points = 1.400000 m= 78139 mr = 118728 m= 25236 mr = 63607 m= 5404 mr = 19950 m= 637 mr = 3908 m= 26 mr = 364 m= 0 mr = 9 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 19473 time to turn everything in is 0.8500000 number of dielectric boundary points 66022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 19794 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) : 1.850664 object centre at (A) : -7.306999 -0.6534996 16.45850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3333659E-02 0.2638510 midg,1,midg; midg,igrid,midg 0.1045198 -3.6527582E-02 1,midg,midg; igrid,midg,midg -1.7210936E-02 0.3686832 gauss-seidel spectral radius is 0.9992321 estimated iterations to convergence 285 setup time was (sec) 1.080000 now iterating at: 20:05:17 rms-change max change #iterations 9.511507 272.6856 at 10iterations 5.447561 120.0238 at 20iterations 3.105615 61.70332 at 30iterations 1.770496 43.04524 at 40iterations 1.007119 22.97511 at 50iterations 0.5740485 10.33049 at 60iterations 0.3258489 6.120967 at 70iterations 0.1853176 3.962498 at 80iterations 0.1049765 1.929215 at 90iterations 5.9777025E-02 1.182447 at 100iterations 3.3931740E-02 0.6521130 at 110iterations 1.9311884E-02 0.3734045 at 120iterations 1.0964156E-02 0.2142487 at 130iterations 6.2238863E-03 0.1215668 at 140iterations 3.5275600E-03 6.6079140E-02 at 150iterations 2.0071371E-03 3.6211014E-02 at 160iterations 1.1378855E-03 2.1842957E-02 at 170iterations 6.4667093E-04 1.3074875E-02 at 180iterations finished qdiffx linear iterations at : 20:05:33 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 6.4667093E-04 1.3074875E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 20:05:33 12.456u 0.357s 0:17.59 72.7% 0+0k 0+0io 0pf+0w