Sun Oct 9 21:11:49 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 Sun Oct 9 2011 at 21:11:49 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3200 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 0.6084742 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): 45.62200 98.68500 ymin,ymax (A): 2.968000 61.47500 zmin,zma (A): 14.85100 66.82800 x,y,z range (A): 53.06300 58.50700 51.97701 scale (grids/A): 0.6084742 object centre (A): 72.15350 32.22150 40.83950 number of atom coordinates read : 3200 total number of charged atoms : 3138 net assigned charge : 5.025015 assigned positive charge : 500.3636 centred at (gu) : 90.22862 87.60942 90.59661 assigned negative charge : -495.3400 centred at (gu) : 90.13966 87.52946 90.60669 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8130 nv = 96 ne = 84 npr = 59775 no. pairs analyzed = 59775 no. exposed pairs = 4406 no. arc points = 32268 no. surface atoms = 1457 nbur = 1743 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4061 m= 3 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2400000 number of dielectric boundary points 4474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3283 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 10211 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1018454E-09 2.6439915E-09 midg,1,midg; midg,igrid,midg -3.4536569E-09 4.5281916E-09 1,midg,midg; igrid,midg,midg -2.3203934E-09 8.6365697E-09 gauss-seidel spectral radius is 0.9860858 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 21:11:49 rms-change max change #iterations 0.1275867 17.76575 at 10iterations 1.1188782E-02 1.503517 at 20iterations 9.8434312E-04 0.1421356 at 30iterations 9.1159258E-05 1.4417648E-02 at 40iterations 1.0447248E-05 1.4953613E-03 at 50iterations finished qdiffx linear iterations at : 21:11:52 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.0447248E-05 1.4953613E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 21:11:53 3.443u 0.161s 0:03.88 92.7% 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 Sun Oct 9 2011 at 21:11:53 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3200 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 1.825423 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): 45.62200 98.68500 ymin,ymax (A): 2.968000 61.47500 zmin,zma (A): 14.85100 66.82800 x,y,z range (A): 53.06300 58.50700 51.97701 scale (grids/A): 1.825423 object centre (A): 72.15350 32.22150 40.83950 number of atom coordinates read : 3200 total number of charged atoms : 3138 net assigned charge : 5.025015 assigned positive charge : 500.3636 centred at (gu) : 90.68494 82.82735 91.78876 assigned negative charge : -495.3400 centred at (gu) : 90.41872 82.58818 91.81933 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 87860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32268 grid for indexing accessible points = 1.400000 m= 29605 mr = 57781 m= 4452 mr = 20364 m= 280 mr = 2487 m= 6 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1720 time to turn everything in is 0.4300000 number of dielectric boundary points 41484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 24578 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) : 0.6084742 object centre at (A) : 72.15350 32.22150 40.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5782477E-03 -2.7087654E-03 midg,1,midg; midg,igrid,midg 4.4737328E-02 2.5871137E-02 1,midg,midg; igrid,midg,midg -1.6190520E-02 1.0789048E-02 gauss-seidel spectral radius is 0.9986000 estimated iterations to convergence 212 setup time was (sec) 0.6500000 now iterating at: 21:11:54 rms-change max change #iterations 4.443192 181.8748 at 10iterations 2.055103 62.52396 at 20iterations 0.9473380 29.50458 at 30iterations 0.4386157 13.45949 at 40iterations 0.2026667 5.985708 at 50iterations 9.3986340E-02 2.755783 at 60iterations 4.3422729E-02 1.301111 at 70iterations 2.0123607E-02 0.5811911 at 80iterations 9.3286708E-03 0.2782522 at 90iterations 4.3243463E-03 0.1296539 at 100iterations 1.9999396E-03 5.8968544E-02 at 110iterations 9.2889473E-04 2.9827118E-02 at 120iterations finished qdiffx linear iterations at : 21:12:01 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 9.2889473E-04 2.9827118E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 21:12:01 8.005u 0.194s 0:08.48 96.5% 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 Sun Oct 9 2011 at 21:12:01 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3200 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.738134 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): 45.62200 98.68500 ymin,ymax (A): 2.968000 61.47500 zmin,zma (A): 14.85100 66.82800 x,y,z range (A): 53.06300 58.50700 51.97701 scale (grids/A): 2.738134 object centre (A): 72.15350 32.22150 40.83950 number of atom coordinates read : 3200 total number of charged atoms : 3138 net assigned charge : 5.025015 assigned positive charge : 500.3636 centred at (gu) : 91.02743 79.24074 92.68307 assigned negative charge : -495.3400 centred at (gu) : 90.62783 78.88213 92.72887 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 203321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32268 grid for indexing accessible points = 1.400000 m= 97254 mr = 141415 m= 33164 mr = 76336 m= 7810 mr = 25296 m= 1047 mr = 5382 m= 72 mr = 633 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 5803 time to turn everything in is 1.060000 number of dielectric boundary points 93576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 25102 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) : 1.825423 object centre at (A) : 72.15350 32.22150 40.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6821781E-02 -0.1559072 midg,1,midg; midg,igrid,midg 0.4384879 0.2940212 1,midg,midg; igrid,midg,midg -0.2051884 0.1157333 gauss-seidel spectral radius is 0.9992754 estimated iterations to convergence 293 setup time was (sec) 1.300000 now iterating at: 21:12:03 rms-change max change #iterations 10.92107 299.7731 at 10iterations 6.557680 158.9784 at 20iterations 3.889009 83.31114 at 30iterations 2.288240 49.36326 at 40iterations 1.342085 30.49746 at 50iterations 0.7876745 15.94062 at 60iterations 0.4604978 8.692120 at 70iterations 0.2679553 5.331560 at 80iterations 0.1560143 2.817513 at 90iterations 9.0532258E-02 1.699966 at 100iterations 5.2600883E-02 0.9565601 at 110iterations 3.0568691E-02 0.6395493 at 120iterations 1.7740348E-02 0.3118255 at 130iterations 1.0262911E-02 0.1880283 at 140iterations 5.9518758E-03 0.1019104 at 150iterations 3.4547606E-03 6.2349319E-02 at 160iterations 2.0014551E-03 3.7091255E-02 at 170iterations 1.1580326E-03 2.0835876E-02 at 180iterations finished qdiffx linear iterations at : 21:12:15 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 1.1580326E-03 2.0835876E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 21:12:15 13.189u 0.241s 0:13.70 97.9% 0+0k 0+0io 0pf+0w