Sat Oct 8 11:48:59 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 Sat Oct 8 2011 at 11:48:59 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4455 !!! WARNING: HIT 440 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5645238 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): -27.06900 35.12600 ymin,ymax (A): 35.04000 98.10201 zmin,zma (A): 30.76900 89.91600 x,y,z range (A): 62.19500 63.06201 59.14700 scale (grids/A): 0.5645238 object centre (A): 4.028500 66.57100 60.34250 number of atom coordinates read : 4455 total number of charged atoms : 4294 net assigned charge : -7.485953 assigned positive charge : 672.8570 centred at (gu) : 90.53146 88.25618 88.86109 assigned negative charge : -680.3463 centred at (gu) : 90.39344 88.30324 89.03825 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8972 nv = 96 ne = 84 npr = 94030 no. pairs analyzed = 94030 no. exposed pairs = 5028 no. arc points = 33946 no. surface atoms = 1712 nbur = 2743 mkacc time = 0.2400000 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 = 1.540000 m= 383 mr = 5184 m= 0 mr = 31 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.4700000 number of dielectric boundary points 4140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3551 ## 406 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11946 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2225929E-09 -3.4947725E-09 midg,1,midg; midg,igrid,midg -9.8937109E-11 -1.2899927E-09 1,midg,midg; igrid,midg,midg -3.3348948E-09 1.9173683E-09 gauss-seidel spectral radius is 0.9839125 estimated iterations to convergence 65 setup time was (sec) 0.8100000 now iterating at: 11:49:01 rms-change max change #iterations 0.1097816 16.94668 at 10iterations 8.5965050E-03 1.175049 at 20iterations 1.0810551E-03 0.1438637 at 30iterations 2.7472730E-04 3.4633636E-02 at 40iterations 8.8682245E-05 1.1130810E-02 at 50iterations finished qdiffx linear iterations at : 11:49:05 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 8.8682245E-05 1.1130810E-02 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.190000 DelPhi exited at 11:49:05 5.198u 0.421s 0:05.90 95.0% 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 11:49:05 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4455 !!! WARNING: HIT 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.693571 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): -27.06900 35.12600 ymin,ymax (A): 35.04000 98.10201 zmin,zma (A): 30.76900 89.91600 x,y,z range (A): 62.19500 63.06201 59.14700 scale (grids/A): 1.693571 object centre (A): 4.028500 66.57100 60.34250 number of atom coordinates read : 4455 total number of charged atoms : 4294 net assigned charge : -7.485953 assigned positive charge : 672.8570 centred at (gu) : 91.59331 84.76729 86.58202 assigned negative charge : -680.3463 centred at (gu) : 91.17995 84.90914 87.11442 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 100802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33946 grid for indexing accessible points = 1.400000 m= 33330 mr = 73177 m= 3968 mr = 24434 m= 123 mr = 2316 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 6770 time to turn everything in is 0.7800000 number of dielectric boundary points 38281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 33128 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) : 0.5645238 object centre at (A) : 4.028500 66.57100 60.34250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8880195E-02 -2.6075585E-02 midg,1,midg; midg,igrid,midg 1.7864157E-02 -5.4618972E-03 1,midg,midg; igrid,midg,midg -2.9678481E-02 2.5733391E-02 gauss-seidel spectral radius is 0.9984383 estimated iterations to convergence 201 setup time was (sec) 1.130000 now iterating at: 11:49:07 rms-change max change #iterations 4.592597 171.3567 at 10iterations 2.036145 63.78480 at 20iterations 0.9095902 25.82505 at 30iterations 0.4042827 14.07204 at 40iterations 0.1798967 5.652883 at 50iterations 8.0328524E-02 2.564127 at 60iterations 3.5890445E-02 0.9656186 at 70iterations 1.6065849E-02 0.4476299 at 80iterations 7.2377906E-03 0.2054386 at 90iterations 3.3034063E-03 0.1059761 at 100iterations 1.5431450E-03 4.3312073E-02 at 110iterations 7.5732474E-04 2.3725510E-02 at 120iterations finished qdiffx linear iterations at : 11:49:18 total time elapsed so far: 12.08000 # loops : 120 mean,max change (kT/e) : 7.5732474E-04 2.3725510E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 11:49:18 12.251u 0.517s 0:13.08 97.5% 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 Sat Oct 8 2011 at 11:49:18 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4455 !!! WARNING: HIT 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.540357 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): -27.06900 35.12600 ymin,ymax (A): 35.04000 98.10201 zmin,zma (A): 30.76900 89.91600 x,y,z range (A): 62.19500 63.06201 59.14700 scale (grids/A): 2.540357 object centre (A): 4.028500 66.57100 60.34250 number of atom coordinates read : 4455 total number of charged atoms : 4294 net assigned charge : -7.485953 assigned positive charge : 672.8570 centred at (gu) : 92.38966 82.15045 84.87254 assigned negative charge : -680.3463 centred at (gu) : 91.76967 82.36362 85.67145 start vw surface at 0.1700000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 234616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33946 grid for indexing accessible points = 1.400000 m= 114636 mr = 177894 m= 35043 mr = 94259 m= 6629 mr = 27770 m= 594 mr = 4928 m= 11 mr = 357 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 23166 time to turn everything in is 2.040000 number of dielectric boundary points 86321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 34328 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) : 1.693571 object centre at (A) : 4.028500 66.57100 60.34250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6926779 -0.3026448 midg,1,midg; midg,igrid,midg 0.3560337 -8.1810169E-02 1,midg,midg; igrid,midg,midg -0.3838243 0.2628323 gauss-seidel spectral radius is 0.9992305 estimated iterations to convergence 285 setup time was (sec) 2.450000 now iterating at: 11:49:21 rms-change max change #iterations 11.37030 377.0226 at 10iterations 6.585192 121.3323 at 20iterations 3.796655 73.08285 at 30iterations 2.181875 38.85087 at 40iterations 1.250958 22.56861 at 50iterations 0.7163843 12.59223 at 60iterations 0.4093456 7.391695 at 70iterations 0.2338911 3.650360 at 80iterations 0.1332870 2.476900 at 90iterations 7.6272391E-02 1.282169 at 100iterations 4.3476347E-02 0.7821242 at 110iterations 2.4822218E-02 0.4060504 at 120iterations 1.4201569E-02 0.2362671 at 130iterations 8.1434930E-03 0.1313324 at 140iterations 4.6850420E-03 8.3305359E-02 at 150iterations 2.7332567E-03 4.9648285E-02 at 160iterations 1.6197888E-03 2.5939941E-02 at 170iterations 9.8780845E-04 1.7322540E-02 at 180iterations finished qdiffx linear iterations at : 11:49:40 total time elapsed so far: 21.33000 # loops : 180 mean,max change (kT/e) : 9.8780845E-04 1.7322540E-02 energy calculations done at 21.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.51000 DelPhi exited at 11:49:41 21.512u 0.503s 0:22.29 98.7% 0+0k 0+0io 0pf+0w