Tue Oct 11 02:39:05 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+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 Tue Oct 11 2011 at 02:39:06 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 0.6660306 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): 20.58800 66.82200 ymin,ymax (A): 14.58000 68.03100 zmin,zma (A): -17.67000 30.23800 x,y,z range (A): 46.23400 53.45100 47.90800 scale (grids/A): 0.6660306 object centre (A): 43.70500 41.30550 6.284000 number of atom coordinates read : 2754 total number of charged atoms : 2615 net assigned charge : 5.420027 assigned positive charge : 424.9152 centred at (gu) : 90.90059 90.22906 90.38145 assigned negative charge : -419.4963 centred at (gu) : 90.72009 90.39536 90.44115 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8259 nv = 96 ne = 84 npr = 56148 no. pairs analyzed = 56148 no. exposed pairs = 3446 no. arc points = 23662 no. surface atoms = 1144 nbur = 1610 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 494 mr = 4720 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3100000 number of dielectric boundary points 3963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2170 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9635 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8468088E-08 1.0210724E-09 midg,1,midg; midg,igrid,midg 5.4080854E-08 -2.7528447E-08 1,midg,midg; igrid,midg,midg -2.4569253E-08 7.2539024E-08 gauss-seidel spectral radius is 0.9883276 estimated iterations to convergence 76 setup time was (sec) 0.5300000 now iterating at: 02:39:06 rms-change max change #iterations 0.1842589 24.58785 at 10iterations 2.0701731E-02 3.094791 at 20iterations 3.2103602E-03 0.5610275 at 30iterations 9.5069775E-04 0.1981583 at 40iterations 3.6022911E-04 7.6663971E-02 at 50iterations finished qdiffx linear iterations at : 02:39:09 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 3.6022911E-04 7.6663971E-02 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 02:39:09 3.109u 0.150s 0:03.90 83.3% 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 Tue Oct 11 2011 at 02:39:10 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 1.998092 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): 20.58800 66.82200 ymin,ymax (A): 14.58000 68.03100 zmin,zma (A): -17.67000 30.23800 x,y,z range (A): 46.23400 53.45100 47.90800 scale (grids/A): 1.998092 object centre (A): 43.70500 41.30550 6.284000 number of atom coordinates read : 2754 total number of charged atoms : 2615 net assigned charge : 5.420027 assigned positive charge : 424.9152 centred at (gu) : 92.70094 90.68626 91.14330 assigned negative charge : -419.4963 centred at (gu) : 92.15983 91.18578 91.32319 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23662 grid for indexing accessible points = 1.400000 m= 33608 mr = 62200 m= 5851 mr = 25331 m= 424 mr = 3875 m= 0 mr = 183 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1220 time to turn everything in is 0.6000000 number of dielectric boundary points 36623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20674 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) : 0.6660306 object centre at (A) : 43.70500 41.30550 6.284000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3197115E-02 -3.1084893E-02 midg,1,midg; midg,igrid,midg 7.6297835E-02 -2.4438212E-02 1,midg,midg; igrid,midg,midg -1.6955376E-02 5.9210189E-02 gauss-seidel spectral radius is 0.9987719 estimated iterations to convergence 226 setup time was (sec) 0.8700000 now iterating at: 02:39:11 rms-change max change #iterations 4.922291 188.7278 at 10iterations 2.395615 84.23471 at 20iterations 1.166228 38.78879 at 30iterations 0.5677640 17.16995 at 40iterations 0.2771968 8.179169 at 50iterations 0.1349090 4.215424 at 60iterations 6.5837771E-02 1.988518 at 70iterations 3.2433443E-02 0.9433403 at 80iterations 1.6109057E-02 0.4855957 at 90iterations 8.1701213E-03 0.2589378 at 100iterations 4.3349415E-03 0.1552773 at 110iterations 2.4516257E-03 9.6801758E-02 at 120iterations finished qdiffx linear iterations at : 02:39:17 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 2.4516257E-03 9.6801758E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 02:39:17 7.080u 0.172s 0:07.71 94.0% 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 Tue Oct 11 2011 at 02:39:17 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 2.997138 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): 20.58800 66.82200 ymin,ymax (A): 14.58000 68.03100 zmin,zma (A): -17.67000 30.23800 x,y,z range (A): 46.23400 53.45100 47.90800 scale (grids/A): 2.997138 object centre (A): 43.70500 41.30550 6.284000 number of atom coordinates read : 2754 total number of charged atoms : 2615 net assigned charge : 5.420027 assigned positive charge : 424.9152 centred at (gu) : 94.05132 91.02906 91.71474 assigned negative charge : -419.4963 centred at (gu) : 93.23969 91.77856 91.98470 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 203961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23662 grid for indexing accessible points = 1.400000 m= 106620 mr = 150347 m= 41276 mr = 88264 m= 10897 mr = 33763 m= 1836 mr = 8429 m= 137 mr = 1299 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 4255 time to turn everything in is 1.530000 number of dielectric boundary points 82557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 20919 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) : 1.998092 object centre at (A) : 43.70500 41.30550 6.284000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2214841 -0.3486215 midg,1,midg; midg,igrid,midg 0.9822922 -0.5291018 1,midg,midg; igrid,midg,midg -0.1997813 0.4712602 gauss-seidel spectral radius is 0.9992954 estimated iterations to convergence 297 setup time was (sec) 1.810000 now iterating at: 02:39:19 rms-change max change #iterations 11.26480 416.7724 at 10iterations 6.665811 128.7745 at 20iterations 3.931029 80.49721 at 30iterations 2.309888 38.23103 at 40iterations 1.359017 24.23048 at 50iterations 0.7970204 16.24155 at 60iterations 0.4670604 8.489807 at 70iterations 0.2735741 4.613880 at 80iterations 0.1600349 2.670383 at 90iterations 9.3566909E-02 1.620218 at 100iterations 5.4789077E-02 0.9257507 at 110iterations 3.2148432E-02 0.5617981 at 120iterations 1.8983416E-02 0.3351212 at 130iterations 1.1334369E-02 0.2179165 at 140iterations 6.9300835E-03 0.1512184 at 150iterations 4.3961313E-03 0.1001358 at 160iterations 2.9532823E-03 6.6497803E-02 at 170iterations 2.1204734E-03 5.2207947E-02 at 180iterations finished qdiffx linear iterations at : 02:39:29 total time elapsed so far: 11.33000 # loops : 180 mean,max change (kT/e) : 2.1204734E-03 5.2207947E-02 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 02:39:30 11.499u 0.194s 0:12.33 94.7% 0+0k 0+0io 0pf+0w