Sun Oct 9 08:11:28 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 Sun Oct 9 2011 at 08:11:28 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: 371 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4421 !!! WARNING: NAP 2099 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.2064067 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): 35.66300 117.6540 ymin,ymax (A): 54.80100 120.4350 zmin,zma (A): 243.6840 416.1590 x,y,z range (A): 81.99100 65.63400 172.4750 scale (grids/A): 0.2064067 object centre (A): 76.65850 87.61800 329.9215 number of atom coordinates read : 4421 total number of charged atoms : 3940 net assigned charge : 11.50003 assigned positive charge : 619.7324 centred at (gu) : 92.76168 89.80672 78.75928 assigned negative charge : -608.2355 centred at (gu) : 92.69389 89.80090 78.87751 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 841 nv = 96 ne = 84 npr = 83091 no. pairs analyzed = 83091 no. exposed pairs = 6251 no. arc points = 45859 no. surface atoms = 2081 nbur = 2340 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 4.270156 m= 13 mr = 211 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 643 no. dielectric boundary points in salt = 14 no. grid points charged and at boundary= 1094 ## 522 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 1347 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5205800E-21 -2.2131525E-27 midg,1,midg; midg,igrid,midg 1.3759163E-25 2.7049860E-25 1,midg,midg; igrid,midg,midg -1.5556699E-25 7.0572388E-24 gauss-seidel spectral radius is 0.8880137 estimated iterations to convergence 27 setup time was (sec) 0.4700000 now iterating at: 08:11:28 rms-change max change #iterations 6.0312450E-04 0.4225063 at 10iterations 2.3118921E-05 2.1589279E-02 at 20iterations 1.0565375E-06 1.0442734E-03 at 30iterations 5.2129980E-08 5.0544739E-05 at 40iterations 7.2340769E-09 3.8146973E-06 at 50iterations finished qdiffx linear iterations at : 08:11:48 total time elapsed so far: 20.07000 # loops : 50 mean,max change (kT/e) : 7.2340769E-09 3.8146973E-06 energy calculations done at 20.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.19000 DelPhi exited at 08:11:48 20.196u 0.173s 0:20.67 98.5% 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 Sun Oct 9 2011 at 08:11:48 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: 371 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4421 !!! WARNING: NAP 2099 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6192201 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): 35.66300 117.6540 ymin,ymax (A): 54.80100 120.4350 zmin,zma (A): 243.6840 416.1590 x,y,z range (A): 81.99100 65.63400 172.4750 scale (grids/A): 0.6192201 object centre (A): 76.65850 87.61800 329.9215 number of atom coordinates read : 4421 total number of charged atoms : 3940 net assigned charge : 11.50003 assigned positive charge : 619.7324 centred at (gu) : 98.28383 89.41921 56.27663 assigned negative charge : -608.2355 centred at (gu) : 98.08132 89.40218 56.63232 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 12177 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45859 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.843840 m= 629 mr = 6034 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 3.9999992E-02 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.1900000 number of dielectric boundary points 6710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3891 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 13373 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) : 0.2064067 object centre at (A) : 76.65850 87.61800 329.9215 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7098086E-04 -2.3506927E-05 midg,1,midg; midg,igrid,midg 4.5908550E-08 1.2723068E-08 1,midg,midg; igrid,midg,midg -5.3110107E-09 9.3099523E-08 gauss-seidel spectral radius is 0.9865555 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 08:11:49 rms-change max change #iterations 0.1613274 27.86192 at 10iterations 1.4767612E-02 2.200531 at 20iterations 1.4186007E-03 0.1820335 at 30iterations 1.8770756E-04 2.1224022E-02 at 40iterations 4.4320572E-05 4.4131279E-03 at 50iterations 1.3057926E-05 1.2726784E-03 at 60iterations 3.9892293E-06 3.7574768E-04 at 70iterations 1.2344312E-06 1.1312962E-04 at 80iterations 3.9190869E-07 3.8146973E-05 at 90iterations 1.6089430E-07 2.2888184E-05 at 100iterations 1.1651394E-07 3.0517578E-05 at 110iterations 1.1121083E-07 3.0517578E-05 at 120iterations finished qdiffx linear iterations at : 08:11:57 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 1.1121083E-07 3.0517578E-05 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 08:11:57 8.150u 0.181s 0:08.60 96.8% 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 Sun Oct 9 2011 at 08:11:57 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: 371 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4421 !!! WARNING: NAP 2099 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.9288302 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): 35.66300 117.6540 ymin,ymax (A): 54.80100 120.4350 zmin,zma (A): 243.6840 416.1590 x,y,z range (A): 81.99100 65.63400 172.4750 scale (grids/A): 0.9288302 object centre (A): 76.65850 87.61800 329.9215 number of atom coordinates read : 4421 total number of charged atoms : 3940 net assigned charge : 11.50003 assigned positive charge : 619.7324 centred at (gu) : 102.4254 89.12833 39.41469 assigned negative charge : -608.2355 centred at (gu) : 102.1219 89.10325 39.94834 start vw surface at 0.1200000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 29771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45859 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.937023 m= 3591 mr = 16712 m= 60 mr = 1370 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 128 time to turn everything in is 0.3200000 number of dielectric boundary points 15340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1642 ## 129 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 21848 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) : 0.6192201 object centre at (A) : 76.65850 87.61800 329.9215 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6213745E-02 -6.4392126E-04 midg,1,midg; midg,igrid,midg 1.2770985E-05 1.1056731E-06 1,midg,midg; igrid,midg,midg -5.0933522E-07 1.3698179E-05 gauss-seidel spectral radius is 0.9939421 estimated iterations to convergence 104 setup time was (sec) 0.5300000 now iterating at: 08:11:58 rms-change max change #iterations 0.9542989 84.39063 at 10iterations 0.2019833 19.37576 at 20iterations 4.2164378E-02 3.666094 at 30iterations 8.7635536E-03 0.7238221 at 40iterations 1.8413344E-03 0.1412601 at 50iterations 4.1467565E-04 3.1600952E-02 at 60iterations 1.1008968E-04 9.5748901E-03 at 70iterations 3.6923775E-05 3.4332275E-03 at 80iterations 1.4550189E-05 1.3790131E-03 at 90iterations 6.1212027E-06 5.7029724E-04 at 100iterations 2.6484047E-06 2.4223328E-04 at 110iterations 1.1843774E-06 1.0681152E-04 at 120iterations 5.8419130E-07 5.3405762E-05 at 130iterations 3.6581565E-07 6.1035156E-05 at 140iterations 2.9966031E-07 3.0517578E-05 at 150iterations 2.9183892E-07 6.1035156E-05 at 160iterations 2.9202118E-07 6.1035156E-05 at 170iterations 2.8992469E-07 6.1035156E-05 at 180iterations finished qdiffx linear iterations at : 08:12:08 total time elapsed so far: 10.85000 # loops : 180 mean,max change (kT/e) : 2.8992469E-07 6.1035156E-05 energy calculations done at 10.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.98000 DelPhi exited at 08:12:09 10.987u 0.193s 0:11.45 97.5% 0+0k 0+0io 0pf+0w