Tue Nov 15 22:08:17 PST 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 Tue Nov 15 2011 at 22:08:17 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= 7.0000000E-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 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6629 nv = 96 ne = 84 npr = 61419 no. pairs analyzed = 61419 no. exposed pairs = 4089 no. arc points = 29949 no. surface atoms = 1378 nbur = 1758 mkacc time = 0.1200000 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= 267 mr = 3298 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2700000 number of dielectric boundary points 3583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3118 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.3300000 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 0.9839622 estimated iterations to convergence 65 setup time was (sec) 0.4700000 now iterating at: 22:08:17 rms-change max change #iterations 8.9459859E-02 15.65914 at 10iterations 6.4960858E-03 1.189007 at 20iterations 4.8562113E-04 7.6164246E-02 at 30iterations 3.7782018E-05 5.6724548E-03 at 40iterations 3.9513848E-06 5.7029724E-04 at 50iterations finished qdiffx linear iterations at : 22:08:20 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 3.9513848E-06 5.7029724E-04 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 22:08:21 3.561u 0.190s 0:04.19 89.4% 0+0k 0+46056io 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 Tue Nov 15 2011 at 22:08:21 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= 7.0000000E-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 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 73413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29949 grid for indexing accessible points = 1.400000 m= 21866 mr = 48520 m= 2489 mr = 14660 m= 105 mr = 1320 m= 1 mr = 18 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 410 time to turn everything in is 0.4400000 number of dielectric boundary points 33357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5200000 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 -2.7853004E-03 1.2469183E-02 midg,1,midg; midg,igrid,midg 2.7175108E-04 6.5472390E-04 1,midg,midg; igrid,midg,midg -2.3578176E-02 9.8958034E-03 gauss-seidel spectral radius is 0.9983537 estimated iterations to convergence 196 setup time was (sec) 0.6600000 now iterating at: 22:08:22 rms-change max change #iterations 3.710916 174.9274 at 10iterations 1.601021 55.98527 at 20iterations 0.6945663 23.11544 at 30iterations 0.3010388 9.881342 at 40iterations 0.1305885 4.465851 at 50iterations 5.6543015E-02 1.796263 at 60iterations 2.4525942E-02 0.8126965 at 70iterations 1.0650834E-02 0.3753271 at 80iterations 4.6374914E-03 0.1537871 at 90iterations 2.0105313E-03 7.4524879E-02 at 100iterations 8.7450858E-04 3.1005859E-02 at 110iterations 3.8055883E-04 1.2962341E-02 at 120iterations finished qdiffx linear iterations at : 22:08:29 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 3.8055883E-04 1.2962341E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 22:08:29 8.025u 0.209s 0:08.55 96.1% 0+0k 0+45336io 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 Tue Nov 15 2011 at 22:08:29 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= 5.9999999E-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 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 170408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29949 grid for indexing accessible points = 1.400000 m= 75860 mr = 118952 m= 21534 mr = 59144 m= 4071 mr = 15896 m= 409 mr = 2824 m= 10 mr = 213 m= 0 mr = 3 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 1379 time to turn everything in is 1.110000 number of dielectric boundary points 75260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.200000 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 -5.2863378E-02 0.2045837 midg,1,midg; midg,igrid,midg 4.2723719E-02 -1.2337862E-02 1,midg,midg; igrid,midg,midg -0.6774330 0.7132443 gauss-seidel spectral radius is 0.9991978 estimated iterations to convergence 279 setup time was (sec) 1.320000 now iterating at: 22:08:31 rms-change max change #iterations 9.507312 307.6084 at 10iterations 5.463390 155.7684 at 20iterations 3.133494 78.17784 at 30iterations 1.782992 43.99314 at 40iterations 1.016776 22.46483 at 50iterations 0.5763640 13.34925 at 60iterations 0.3264427 6.567455 at 70iterations 0.1841185 3.780364 at 80iterations 0.1040422 2.289090 at 90iterations 5.8742359E-02 1.297470 at 100iterations 3.3029277E-02 0.6518002 at 110iterations 1.8656610E-02 0.3841057 at 120iterations 1.0496631E-02 0.2145561 at 130iterations 5.8885957E-03 0.1141191 at 140iterations 3.3223960E-03 6.4308643E-02 at 150iterations 1.8647191E-03 3.4875870E-02 at 160iterations 1.0479968E-03 2.3457289E-02 at 170iterations 5.9143506E-04 1.1119843E-02 at 180iterations finished qdiffx linear iterations at : 22:08:42 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 5.9143506E-04 1.1119843E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 22:08:43 12.938u 0.230s 0:13.51 97.4% 0+0k 0+45328io 0pf+0w