Mon Oct 10 14:39:53 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 14:39:53 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 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: 0.6704963 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): -21.78100 31.31400 ymin,ymax (A): 12.10400 57.99800 zmin,zma (A): 27.96100 78.26200 x,y,z range (A): 53.09500 45.89400 50.30100 scale (grids/A): 0.6704963 object centre (A): 4.766500 35.05100 53.11150 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.1852 centred at (gu) : 89.38589 90.68959 90.31360 assigned negative charge : -361.6858 centred at (gu) : 89.56557 90.68001 90.39175 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7213 nv = 96 ne = 84 npr = 49061 no. pairs analyzed = 49061 no. exposed pairs = 2906 no. arc points = 20542 no. surface atoms = 990 nbur = 1374 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 4040 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2800000 number of dielectric boundary points 3537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1912 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8396 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1973986E-09 -3.2944332E-08 midg,1,midg; midg,igrid,midg -1.2436631E-08 -1.1058043E-08 1,midg,midg; igrid,midg,midg 3.4682635E-08 -4.9287021E-08 gauss-seidel spectral radius is 0.9884497 estimated iterations to convergence 76 setup time was (sec) 0.5300000 now iterating at: 14:39:54 rms-change max change #iterations 0.1706842 24.37700 at 10iterations 1.9154167E-02 2.877216 at 20iterations 2.1297475E-03 0.2808371 at 30iterations 2.5264319E-04 4.0630341E-02 at 40iterations 3.8444196E-05 7.7800751E-03 at 50iterations finished qdiffx linear iterations at : 14:39:57 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.8444196E-05 7.7800751E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:39:57 3.429u 0.208s 0:03.93 92.1% 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 14:39:57 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.011489 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): -21.78100 31.31400 ymin,ymax (A): 12.10400 57.99800 zmin,zma (A): 27.96100 78.26200 x,y,z range (A): 53.09500 45.89400 50.30100 scale (grids/A): 2.011489 object centre (A): 4.766500 35.05100 53.11150 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.1852 centred at (gu) : 88.15723 92.06847 90.94037 assigned negative charge : -361.6858 centred at (gu) : 88.69660 92.03989 91.17509 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77017 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20542 grid for indexing accessible points = 1.400000 m= 28978 mr = 53730 m= 5321 mr = 21592 m= 435 mr = 3520 m= 8 mr = 203 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 551 time to turn everything in is 0.6100000 number of dielectric boundary points 32714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17655 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) : 0.6704963 object centre at (A) : 4.766500 35.05100 53.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8736832E-02 -4.2998701E-02 midg,1,midg; midg,igrid,midg -1.1218018E-02 -6.1919115E-04 1,midg,midg; igrid,midg,midg 3.1388734E-02 -6.1307964E-03 gauss-seidel spectral radius is 0.9987499 estimated iterations to convergence 224 setup time was (sec) 0.8800000 now iterating at: 14:39:58 rms-change max change #iterations 4.533545 201.1902 at 10iterations 2.191181 70.91327 at 20iterations 1.054143 32.87926 at 30iterations 0.5109961 15.53619 at 40iterations 0.2472011 7.308800 at 50iterations 0.1194843 3.425373 at 60iterations 5.7689711E-02 1.813110 at 70iterations 2.8010074E-02 0.8860388 at 80iterations 1.3542728E-02 0.3949165 at 90iterations 6.5540480E-03 0.1826694 at 100iterations 3.1990106E-03 9.1545105E-02 at 110iterations 1.5477245E-03 4.5474529E-02 at 120iterations finished qdiffx linear iterations at : 14:40:05 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 1.5477245E-03 4.5474529E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 14:40:05 7.458u 0.194s 0:08.01 95.3% 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 Mon Oct 10 2011 at 14:40:05 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 3.017233 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): -21.78100 31.31400 ymin,ymax (A): 12.10400 57.99800 zmin,zma (A): 27.96100 78.26200 x,y,z range (A): 53.09500 45.89400 50.30100 scale (grids/A): 3.017233 object centre (A): 4.766500 35.05100 53.11150 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.1852 centred at (gu) : 87.23571 93.10246 91.41053 assigned negative charge : -361.6858 centred at (gu) : 88.04491 93.05995 91.76262 start vw surface at 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 177975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20542 grid for indexing accessible points = 1.400000 m= 91519 mr = 129844 m= 35789 mr = 75448 m= 10047 mr = 29127 m= 1880 mr = 7786 m= 174 mr = 1346 m= 5 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 1885 time to turn everything in is 1.500000 number of dielectric boundary points 73755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 17848 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) : 2.011489 object centre at (A) : 4.766500 35.05100 53.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4256976 -0.2376435 midg,1,midg; midg,igrid,midg -3.3536050E-02 0.1299589 1,midg,midg; igrid,midg,midg 0.3282705 1.4187085E-02 gauss-seidel spectral radius is 0.9992816 estimated iterations to convergence 294 setup time was (sec) 1.830000 now iterating at: 14:40:07 rms-change max change #iterations 10.44108 336.3209 at 10iterations 6.146478 148.2062 at 20iterations 3.610114 70.11481 at 30iterations 2.112717 47.27487 at 40iterations 1.232475 27.14157 at 50iterations 0.7196341 12.58092 at 60iterations 0.4198255 8.298678 at 70iterations 0.2440812 4.740692 at 80iterations 0.1416148 2.766808 at 90iterations 8.2440421E-02 1.496456 at 100iterations 4.7851667E-02 0.7794781 at 110iterations 2.7878018E-02 0.5611358 at 120iterations 1.6172014E-02 0.2908688 at 130iterations 9.3996441E-03 0.1543112 at 140iterations 5.4832962E-03 9.4776630E-02 at 150iterations 3.2101895E-03 5.5500031E-02 at 160iterations 1.8862181E-03 3.4090996E-02 at 170iterations 1.1234160E-03 2.1821976E-02 at 180iterations finished qdiffx linear iterations at : 14:40:18 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.1234160E-03 2.1821976E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 14:40:19 13.049u 0.261s 0:14.02 94.8% 0+0k 0+0io 0pf+0w