Mon Oct 10 09:45:48 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 Mon Oct 10 2011 at 09:45:48 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2916 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5680459 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): -17.83000 33.60900 ymin,ymax (A): -59.46100 -0.9910001 zmin,zma (A): -2.312000 60.35900 x,y,z range (A): 51.43900 58.47000 62.67100 scale (grids/A): 0.5680459 object centre (A): 7.889499 -30.22600 29.02350 number of atom coordinates read : 2916 total number of charged atoms : 2763 net assigned charge : 8.014026 assigned positive charge : 427.6487 centred at (gu) : 88.86835 88.13701 87.93466 assigned negative charge : -419.6353 centred at (gu) : 88.98721 87.98711 87.78889 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6405 nv = 96 ne = 84 npr = 55822 no. pairs analyzed = 55822 no. exposed pairs = 4483 no. arc points = 32646 no. surface atoms = 1480 nbur = 1436 mkacc time = 0.1900000 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 = 1.512000 m= 264 mr = 2708 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3212 ## 383 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 8064 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4205233E-09 1.9471447E-09 midg,1,midg; midg,igrid,midg -1.4388153E-09 2.0759825E-09 1,midg,midg; igrid,midg,midg 3.6862753E-09 -3.2732800E-10 gauss-seidel spectral radius is 0.9840273 estimated iterations to convergence 65 setup time was (sec) 0.7500000 now iterating at: 09:45:49 rms-change max change #iterations 8.6390994E-02 13.81997 at 10iterations 6.3301544E-03 1.067848 at 20iterations 4.8517657E-04 8.0234528E-02 at 30iterations 4.5627607E-05 7.0266724E-03 at 40iterations 7.1958830E-06 8.6784363E-04 at 50iterations finished qdiffx linear iterations at : 09:45:53 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 7.1958830E-06 8.6784363E-04 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 09:45:53 4.513u 0.451s 0:05.36 92.5% 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 Mon Oct 10 2011 at 09:45:54 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2916 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.704138 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): -17.83000 33.60900 ymin,ymax (A): -59.46100 -0.9910001 zmin,zma (A): -2.312000 60.35900 x,y,z range (A): 51.43900 58.47000 62.67100 scale (grids/A): 1.704138 object centre (A): 7.889499 -30.22600 29.02350 number of atom coordinates read : 2916 total number of charged atoms : 2763 net assigned charge : 8.014026 assigned positive charge : 427.6487 centred at (gu) : 86.60452 84.41032 83.80345 assigned negative charge : -419.6353 centred at (gu) : 86.96119 83.96096 83.36612 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 68208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32646 grid for indexing accessible points = 1.400000 m= 20748 mr = 40835 m= 2577 mr = 12943 m= 83 mr = 1094 m= 3 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 36741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21446 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) : 0.5680459 object centre at (A) : 7.889499 -30.22600 29.02350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0083268E-02 7.6004248E-03 midg,1,midg; midg,igrid,midg 1.8540017E-02 2.9589778E-02 1,midg,midg; igrid,midg,midg 1.1645250E-02 4.0600793E-03 gauss-seidel spectral radius is 0.9983591 estimated iterations to convergence 196 setup time was (sec) 1.080000 now iterating at: 09:45:55 rms-change max change #iterations 3.572830 195.5102 at 10iterations 1.545129 67.10877 at 20iterations 0.6741672 28.65494 at 30iterations 0.2928023 10.99544 at 40iterations 0.1270888 4.669133 at 50iterations 5.5239078E-02 2.244562 at 60iterations 2.4009882E-02 0.8651848 at 70iterations 1.0419253E-02 0.3517914 at 80iterations 4.5425692E-03 0.1747235 at 90iterations 1.9783757E-03 7.0663452E-02 at 100iterations 8.6172903E-04 3.0963795E-02 at 110iterations 3.7570589E-04 1.3471603E-02 at 120iterations finished qdiffx linear iterations at : 09:46:04 total time elapsed so far: 10.13000 # loops : 120 mean,max change (kT/e) : 3.7570589E-04 1.3471603E-02 energy calculations done at 10.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.34000 DelPhi exited at 09:46:05 10.342u 0.479s 0:11.18 96.6% 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 09:46:05 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2916 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.556206 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): -17.83000 33.60900 ymin,ymax (A): -59.46100 -0.9910001 zmin,zma (A): -2.312000 60.35900 x,y,z range (A): 51.43900 58.47000 62.67100 scale (grids/A): 2.556206 object centre (A): 7.889499 -30.22600 29.02350 number of atom coordinates read : 2916 total number of charged atoms : 2763 net assigned charge : 8.014026 assigned positive charge : 427.6487 centred at (gu) : 84.90648 81.61527 80.70509 assigned negative charge : -419.6353 centred at (gu) : 85.44177 80.94125 80.04903 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 157862 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32646 grid for indexing accessible points = 1.400000 m= 68240 mr = 101328 m= 21573 mr = 50070 m= 3968 mr = 15064 m= 248 mr = 2319 m= 3 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 83033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 22094 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) : 1.704138 object centre at (A) : 7.889499 -30.22600 29.02350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2450794 1.2733012E-02 midg,1,midg; midg,igrid,midg 0.4175809 0.3741627 1,midg,midg; igrid,midg,midg 6.3578486E-02 4.6898220E-02 gauss-seidel spectral radius is 0.9992100 estimated iterations to convergence 281 setup time was (sec) 2.150000 now iterating at: 09:46:07 rms-change max change #iterations 9.215527 301.8191 at 10iterations 5.433178 153.9964 at 20iterations 3.163365 80.32100 at 30iterations 1.821347 45.17907 at 40iterations 1.046997 25.99339 at 50iterations 0.5978371 13.68825 at 60iterations 0.3412531 8.982780 at 70iterations 0.1937820 4.155418 at 80iterations 0.1100126 2.326456 at 90iterations 6.2450282E-02 1.699545 at 100iterations 3.5376355E-02 0.7838955 at 110iterations 1.9987712E-02 0.4215069 at 120iterations 1.1298642E-02 0.3326855 at 130iterations 6.3807308E-03 0.1277771 at 140iterations 3.6056323E-03 8.0851078E-02 at 150iterations 2.0327263E-03 4.9442530E-02 at 160iterations 1.1505703E-03 2.3590088E-02 at 170iterations 6.4799725E-04 1.4142990E-02 at 180iterations finished qdiffx linear iterations at : 09:46:24 total time elapsed so far: 18.46000 # loops : 180 mean,max change (kT/e) : 6.4799725E-04 1.4142990E-02 energy calculations done at 18.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.67000 DelPhi exited at 09:46:24 18.672u 0.530s 0:19.48 98.5% 0+0k 0+0io 0pf+0w