Wed Feb 15 08:56:36 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:36 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3136 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: 0.5668248 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): -25.58100 37.22500 ymin,ymax (A): 6.964000 63.28300 zmin,zma (A): -26.85200 28.09500 x,y,z range (A): 62.80600 56.31900 54.94700 scale (grids/A): 0.5668248 object centre (A): 5.822001 35.12350 0.6214991 number of atom coordinates read : 3136 total number of charged atoms : 2988 net assigned charge : 2.000018 assigned positive charge : 475.4372 centred at (gu) : 92.40097 91.39397 89.36385 assigned negative charge : -473.4379 centred at (gu) : 92.44390 91.46461 89.32770 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6558 nv = 96 ne = 84 npr = 62776 no. pairs analyzed = 62776 no. exposed pairs = 4138 no. arc points = 30415 no. surface atoms = 1395 nbur = 1741 mkacc time = 0.1800000 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= 268 mr = 3192 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3900000 number of dielectric boundary points 3618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3165 ## 419 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8645 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7093541E-10 7.2412720E-10 midg,1,midg; midg,igrid,midg 9.6623143E-10 -1.0602178E-09 1,midg,midg; igrid,midg,midg 5.3418453E-10 -6.1409555E-10 gauss-seidel spectral radius is 0.9839616 estimated iterations to convergence 65 setup time was (sec) 0.6500000 now iterating at: 08:56:37 rms-change max change #iterations 8.8555418E-02 15.67445 at 10iterations 6.4142328E-03 1.168224 at 20iterations 4.7933881E-04 7.3795319E-02 at 30iterations 3.6255497E-05 6.0768127E-03 at 40iterations 3.1972979E-06 4.5204163E-04 at 50iterations finished qdiffx linear iterations at : 08:56:40 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 3.1972979E-06 4.5204163E-04 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 08:56:41 4.108u 0.266s 0:05.13 84.9% 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 Wed Feb 15 2012 at 08:56:41 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3136 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: 1.700474 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): -25.58100 37.22500 ymin,ymax (A): 6.964000 63.28300 zmin,zma (A): -26.85200 28.09500 x,y,z range (A): 62.80600 56.31900 54.94700 scale (grids/A): 1.700474 object centre (A): 5.822001 35.12350 0.6214991 number of atom coordinates read : 3136 total number of charged atoms : 2988 net assigned charge : 2.000018 assigned positive charge : 475.4372 centred at (gu) : 97.20243 94.18103 88.09074 assigned negative charge : -473.4379 centred at (gu) : 97.33127 94.39339 87.98270 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30415 grid for indexing accessible points = 1.400000 m= 21604 mr = 47462 m= 2491 mr = 14299 m= 107 mr = 1309 m= 1 mr = 19 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 146 time to turn everything in is 0.6300000 number of dielectric boundary points 33718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 325 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23103 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) : 0.5668248 object centre at (A) : 5.822001 35.12350 0.6214991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9066517E-03 1.2456328E-02 midg,1,midg; midg,igrid,midg 3.1372323E-04 7.0277991E-04 1,midg,midg; igrid,midg,midg -2.3680827E-02 1.0145433E-02 gauss-seidel spectral radius is 0.9983537 estimated iterations to convergence 196 setup time was (sec) 0.9300000 now iterating at: 08:56:42 rms-change max change #iterations 3.707873 174.9274 at 10iterations 1.599587 55.98524 at 20iterations 0.6931540 25.07118 at 30iterations 0.3004798 9.923679 at 40iterations 0.1301851 4.459644 at 50iterations 5.6472421E-02 1.836221 at 60iterations 2.4437847E-02 0.7784042 at 70iterations 1.0587079E-02 0.3860779 at 80iterations 4.6211020E-03 0.1680830 at 90iterations 2.0025086E-03 9.0395927E-02 at 100iterations 8.6860341E-04 3.5373688E-02 at 110iterations 3.7789420E-04 1.2123108E-02 at 120iterations finished qdiffx linear iterations at : 08:56:51 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 3.7789420E-04 1.2123108E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 08:56:51 9.353u 0.301s 0:10.07 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 Wed Feb 15 2012 at 08:56:51 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3136 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: 2.550712 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): -25.58100 37.22500 ymin,ymax (A): 6.964000 63.28300 zmin,zma (A): -26.85200 28.09500 x,y,z range (A): 62.80600 56.31900 54.94700 scale (grids/A): 2.550712 object centre (A): 5.822001 35.12350 0.6214991 number of atom coordinates read : 3136 total number of charged atoms : 2988 net assigned charge : 2.000018 assigned positive charge : 475.4372 centred at (gu) : 100.8035 96.27156 87.13599 assigned negative charge : -473.4379 centred at (gu) : 100.9968 96.58999 86.97401 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 168294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30415 grid for indexing accessible points = 1.400000 m= 74727 mr = 116302 m= 21288 mr = 57819 m= 4052 mr = 15583 m= 414 mr = 2814 m= 10 mr = 219 m= 0 mr = 3 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 468 time to turn everything in is 1.570000 number of dielectric boundary points 76045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 23886 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) : 1.700474 object centre at (A) : 5.822001 35.12350 0.6214991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6082316E-02 0.2048868 midg,1,midg; midg,igrid,midg 4.3083977E-02 -1.1474556E-02 1,midg,midg; igrid,midg,midg -0.6784461 0.7173074 gauss-seidel spectral radius is 0.9992004 estimated iterations to convergence 279 setup time was (sec) 1.890000 now iterating at: 08:56:54 rms-change max change #iterations 9.542665 307.8854 at 10iterations 5.500447 155.5043 at 20iterations 3.164237 88.00793 at 30iterations 1.806170 46.32813 at 40iterations 1.031907 23.43934 at 50iterations 0.5856447 11.76107 at 60iterations 0.3321923 6.461826 at 70iterations 0.1878496 3.494700 at 80iterations 0.1062774 2.592552 at 90iterations 6.0190879E-02 1.466184 at 100iterations 3.3888876E-02 0.6669703 at 110iterations 1.9151665E-02 0.3773346 at 120iterations 1.0797398E-02 0.2097113 at 130iterations 6.0648448E-03 0.1220753 at 140iterations 3.4207159E-03 6.4735889E-02 at 150iterations 1.9241773E-03 3.9361000E-02 at 160iterations 1.0819002E-03 2.1378517E-02 at 170iterations 6.0939492E-04 1.1296272E-02 at 180iterations finished qdiffx linear iterations at : 08:57:07 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 6.0939492E-04 1.1296272E-02 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.63000 DelPhi exited at 08:57:08 15.633u 0.310s 0:16.45 96.8% 0+0k 0+0io 0pf+0w