Sat Oct 8 20:40:23 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 Sat Oct 8 2011 at 20:40:23 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! 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 607 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6203712 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): -32.33500 17.55100 ymin,ymax (A): -24.09900 22.67500 zmin,zma (A): -12.40000 44.98500 x,y,z range (A): 49.88600 46.77400 57.38500 scale (grids/A): 0.6203712 object centre (A): -7.391999 -0.7119999 16.29250 number of atom coordinates read : 2587 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.71004 89.34109 89.66182 assigned negative charge : -388.8955 centred at (gu) : 88.59816 89.37360 89.55635 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6618 nv = 96 ne = 84 npr = 53182 no. pairs analyzed = 53182 no. exposed pairs = 2998 no. arc points = 21895 no. surface atoms = 1010 nbur = 1577 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3745 m= 0 mr = 44 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 0.2900000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6674686E-09 1.0013015E-08 midg,1,midg; midg,igrid,midg 6.8813137E-09 1.4001812E-09 1,midg,midg; igrid,midg,midg -5.1992477E-09 8.4510203E-09 gauss-seidel spectral radius is 0.9865407 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 20:40:24 rms-change max change #iterations 0.1268086 18.27820 at 10iterations 1.1472237E-02 1.621834 at 20iterations 1.0742451E-03 0.1577759 at 30iterations 9.7788681E-05 1.5783310E-02 at 40iterations 9.1290267E-06 1.4495850E-03 at 50iterations finished qdiffx linear iterations at : 20:40:26 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 9.1290267E-06 1.4495850E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 20:40:27 3.140u 0.157s 0:03.62 90.8% 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 Sat Oct 8 2011 at 20:40:27 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! 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 607 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: 1.861113 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): -32.33500 17.55100 ymin,ymax (A): -24.09900 22.67500 zmin,zma (A): -12.40000 44.98500 x,y,z range (A): 49.88600 46.77400 57.38500 scale (grids/A): 1.861113 object centre (A): -7.391999 -0.7119999 16.29250 number of atom coordinates read : 2587 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 86.12954 88.02299 88.98512 assigned negative charge : -388.8955 centred at (gu) : 85.79416 88.12051 88.66870 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21895 grid for indexing accessible points = 1.400000 m= 25588 mr = 50230 m= 3690 mr = 19128 m= 201 mr = 2350 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5082 time to turn everything in is 0.5200000 number of dielectric boundary points 29405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19343 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) : 0.6203712 object centre at (A) : -7.391999 -0.7119999 16.29250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5186630E-02 2.1706678E-02 midg,1,midg; midg,igrid,midg 8.6572748E-03 5.1816762E-03 1,midg,midg; igrid,midg,midg -4.6414011E-03 4.4222575E-02 gauss-seidel spectral radius is 0.9985700 estimated iterations to convergence 210 setup time was (sec) 0.7900000 now iterating at: 20:40:28 rms-change max change #iterations 4.020929 163.1514 at 10iterations 1.845105 63.21049 at 20iterations 0.8488846 27.46928 at 30iterations 0.3904498 12.77411 at 40iterations 0.1800478 6.202827 at 50iterations 8.2918629E-02 2.680222 at 60iterations 3.8114466E-02 1.231325 at 70iterations 1.7528066E-02 0.5602913 at 80iterations 8.0564376E-03 0.2565918 at 90iterations 3.7186586E-03 0.1142349 at 100iterations 1.7069443E-03 5.9124231E-02 at 110iterations 7.8973186E-04 2.6557922E-02 at 120iterations finished qdiffx linear iterations at : 20:40:34 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 7.8973186E-04 2.6557922E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 20:40:34 6.969u 0.176s 0:07.44 95.8% 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 Sat Oct 8 2011 at 20:40:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! 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 607 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.791670 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): -32.33500 17.55100 ymin,ymax (A): -24.09900 22.67500 zmin,zma (A): -12.40000 44.98500 x,y,z range (A): 49.88600 46.77400 57.38500 scale (grids/A): 2.791670 object centre (A): -7.391999 -0.7119999 16.29250 number of atom coordinates read : 2587 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 84.19411 87.03439 88.47761 assigned negative charge : -388.8955 centred at (gu) : 83.69130 87.18073 88.00303 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 165823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21895 grid for indexing accessible points = 1.400000 m= 84036 mr = 121380 m= 29439 mr = 69768 m= 6578 mr = 23677 m= 903 mr = 4991 m= 55 mr = 618 m= 0 mr = 23 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 16955 time to turn everything in is 1.200000 number of dielectric boundary points 66377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 19726 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) : 1.861113 object centre at (A) : -7.391999 -0.7119999 16.29250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1059525 0.2610457 midg,1,midg; midg,igrid,midg 9.9312887E-02 5.5622865E-02 1,midg,midg; igrid,midg,midg -4.1512921E-02 0.6040836 gauss-seidel spectral radius is 0.9992347 estimated iterations to convergence 285 setup time was (sec) 1.480000 now iterating at: 20:40:36 rms-change max change #iterations 9.448397 323.6349 at 10iterations 5.408237 111.2930 at 20iterations 3.087749 77.72353 at 30iterations 1.760905 33.81661 at 40iterations 1.003996 23.64447 at 50iterations 0.5710589 12.77529 at 60iterations 0.3254070 6.438252 at 70iterations 0.1846742 3.668436 at 80iterations 0.1052673 2.040089 at 90iterations 5.9720684E-02 1.163166 at 100iterations 3.4031700E-02 0.6663907 at 110iterations 1.9351060E-02 0.3639431 at 120iterations 1.0982621E-02 0.2191534 at 130iterations 6.2540574E-03 0.1152000 at 140iterations 3.5565416E-03 6.5580368E-02 at 150iterations 2.0225572E-03 3.4234524E-02 at 160iterations 1.1496224E-03 2.0162582E-02 at 170iterations 6.5313588E-04 1.3319016E-02 at 180iterations finished qdiffx linear iterations at : 20:40:45 total time elapsed so far: 10.95000 # loops : 180 mean,max change (kT/e) : 6.5313588E-04 1.3319016E-02 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 20:40:46 11.123u 0.185s 0:11.57 97.6% 0+0k 0+0io 0pf+0w