Mon Oct 10 16:04:45 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 16:04:45 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 = 4352 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 848 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: 0.5491200 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): -20.14300 31.30200 ymin,ymax (A): -34.26000 29.61600 zmin,zma (A): -29.26200 35.56900 x,y,z range (A): 51.44500 63.87600 64.83100 scale (grids/A): 0.5491200 object centre (A): 5.579500 -2.322001 3.153501 number of atom coordinates read : 4352 total number of charged atoms : 4206 net assigned charge : 3.700016 assigned positive charge : 651.3838 centred at (gu) : 90.19113 90.24394 88.62838 assigned negative charge : -647.6873 centred at (gu) : 90.21664 90.27934 88.58349 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8492 nv = 96 ne = 84 npr = 88472 no. pairs analyzed = 88472 no. exposed pairs = 5264 no. arc points = 36044 no. surface atoms = 1772 nbur = 2580 mkacc time = 0.2300000 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 = 1.568000 m= 366 mr = 4734 m= 0 mr = 25 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3636 ## 463 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11191 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1892386E-10 5.3908594E-10 midg,1,midg; midg,igrid,midg 6.1385702E-10 -1.2533206E-10 1,midg,midg; igrid,midg,midg 5.2021570E-10 -9.9047793E-12 gauss-seidel spectral radius is 0.9829990 estimated iterations to convergence 63 setup time was (sec) 0.7400000 now iterating at: 16:04:46 rms-change max change #iterations 9.3951322E-02 13.69854 at 10iterations 6.5761204E-03 0.9433842 at 20iterations 5.9664098E-04 9.8876953E-02 at 30iterations 1.2863317E-04 2.4553299E-02 at 40iterations 4.2890566E-05 6.9713593E-03 at 50iterations finished qdiffx linear iterations at : 16:04:50 total time elapsed so far: 4.540000 # loops : 50 mean,max change (kT/e) : 4.2890566E-05 6.9713593E-03 energy calculations done at 4.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 16:04:50 4.709u 0.377s 0:05.41 93.7% 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 16:04:50 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 = 4352 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 848 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: 1.647360 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): -20.14300 31.30200 ymin,ymax (A): -34.26000 29.61600 zmin,zma (A): -29.26200 35.56900 x,y,z range (A): 51.44500 63.87600 64.83100 scale (grids/A): 1.647360 object centre (A): 5.579500 -2.322001 3.153501 number of atom coordinates read : 4352 total number of charged atoms : 4206 net assigned charge : 3.700016 assigned positive charge : 651.3838 centred at (gu) : 90.57227 90.73000 85.88338 assigned negative charge : -647.6873 centred at (gu) : 90.64917 90.83765 85.75006 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 95320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36044 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 31144 mr = 67897 m= 3367 mr = 21920 m= 100 mr = 1776 m= 0 mr = 9 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 183 time to turn everything in is 0.7700000 number of dielectric boundary points 38329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 354 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 32233 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) : 0.5491200 object centre at (A) : 5.579500 -2.322001 3.153501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2734061E-02 -5.2354289E-03 midg,1,midg; midg,igrid,midg 2.0335844E-02 1.6564580E-02 1,midg,midg; igrid,midg,midg -4.4310355E-04 5.8521313E-04 gauss-seidel spectral radius is 0.9983553 estimated iterations to convergence 196 setup time was (sec) 1.080000 now iterating at: 16:04:52 rms-change max change #iterations 4.198857 163.6100 at 10iterations 1.824300 64.69367 at 20iterations 0.7931336 26.80848 at 30iterations 0.3455960 10.58971 at 40iterations 0.1503763 4.892939 at 50iterations 6.5556504E-02 2.050295 at 60iterations 2.8688859E-02 0.8862734 at 70iterations 1.2512448E-02 0.3622437 at 80iterations 5.4729101E-03 0.1703377 at 90iterations 2.4011564E-03 6.9347382E-02 at 100iterations 1.0600274E-03 3.3241987E-02 at 110iterations 4.7436953E-04 1.2573242E-02 at 120iterations finished qdiffx linear iterations at : 16:05:02 total time elapsed so far: 11.14000 # loops : 120 mean,max change (kT/e) : 4.7436953E-04 1.2573242E-02 energy calculations done at 11.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 16:05:02 11.306u 0.450s 0:12.02 97.7% 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 16:05:02 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 848 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: 2.471040 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): -20.14300 31.30200 ymin,ymax (A): -34.26000 29.61600 zmin,zma (A): -29.26200 35.56900 x,y,z range (A): 51.44500 63.87600 64.83100 scale (grids/A): 2.471040 object centre (A): 5.579500 -2.322001 3.153501 number of atom coordinates read : 4352 total number of charged atoms : 4206 net assigned charge : 3.700016 assigned positive charge : 651.3838 centred at (gu) : 90.85785 91.09475 83.82468 assigned negative charge : -647.6873 centred at (gu) : 90.97359 91.25632 83.62476 start vw surface at 0.1500000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 221889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36044 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106698 mr = 166010 m= 31595 mr = 85630 m= 5370 mr = 24167 m= 403 mr = 3602 m= 8 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 566 time to turn everything in is 1.940000 number of dielectric boundary points 86360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 33621 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) : 1.647360 object centre at (A) : 5.579500 -2.322001 3.153501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5043737 -0.1206461 midg,1,midg; midg,igrid,midg 0.2912852 0.3391096 1,midg,midg; igrid,midg,midg 1.4270866E-02 1.5727596E-02 gauss-seidel spectral radius is 0.9992206 estimated iterations to convergence 283 setup time was (sec) 2.290000 now iterating at: 16:05:05 rms-change max change #iterations 10.80706 353.3160 at 10iterations 6.305928 133.9142 at 20iterations 3.666258 74.67036 at 30iterations 2.117373 41.14265 at 40iterations 1.218307 21.34106 at 50iterations 0.7002206 13.32640 at 60iterations 0.4009470 7.098513 at 70iterations 0.2290111 3.834641 at 80iterations 0.1309825 2.215973 at 90iterations 7.4655294E-02 1.238079 at 100iterations 4.2460751E-02 0.7547054 at 110iterations 2.4177589E-02 0.4106083 at 120iterations 1.3764820E-02 0.2382202 at 130iterations 7.8428248E-03 0.1350403 at 140iterations 4.4699004E-03 8.1342697E-02 at 150iterations 2.5506727E-03 4.3922424E-02 at 160iterations 1.4683820E-03 2.5700569E-02 at 170iterations 8.5362326E-04 1.4083862E-02 at 180iterations finished qdiffx linear iterations at : 16:05:22 total time elapsed so far: 18.93000 # loops : 180 mean,max change (kT/e) : 8.5362326E-04 1.4083862E-02 energy calculations done at 18.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.08000 DelPhi exited at 16:05:22 19.087u 0.479s 0:20.09 97.3% 0+0k 0+0io 0pf+0w