Wed Dec 28 11:04:49 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+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 Wed Dec 28 2011 at 11:04:49 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6390579 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): -4.544000 35.26700 ymin,ymax (A): -3.621000 47.91800 zmin,zma (A): -23.58300 32.12400 x,y,z range (A): 39.81100 51.53900 55.70700 scale (grids/A): 0.6390579 object centre (A): 15.36150 22.14850 4.270500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 292.1999 centred at (gu) : 90.31014 92.65941 89.59447 assigned negative charge : -290.2002 centred at (gu) : 90.43281 92.82500 89.51596 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5450 nv = 96 ne = 84 npr = 40260 no. pairs analyzed = 40260 no. exposed pairs = 2478 no. arc points = 17455 no. surface atoms = 849 nbur = 1121 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 284 mr = 2975 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2700000 number of dielectric boundary points 2721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1758 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6776073E-09 9.0488248E-09 midg,1,midg; midg,igrid,midg 9.6562376E-09 -1.9828311E-08 1,midg,midg; igrid,midg,midg 1.2634879E-08 -7.6655295E-09 gauss-seidel spectral radius is 0.9872591 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 11:04:50 rms-change max change #iterations 0.1217710 20.91161 at 10iterations 1.2106474E-02 1.886555 at 20iterations 1.1633385E-03 0.2063789 at 30iterations 1.1322747E-04 1.8315315E-02 at 40iterations 1.1396189E-05 1.6555786E-03 at 50iterations finished qdiffx linear iterations at : 11:04:53 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 1.1396189E-05 1.6555786E-03 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 11:04:54 3.804u 0.191s 0:04.31 92.5% 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 Wed Dec 28 2011 at 11:04:54 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.917174 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): -4.544000 35.26700 ymin,ymax (A): -3.621000 47.91800 zmin,zma (A): -23.58300 32.12400 x,y,z range (A): 39.81100 51.53900 55.70700 scale (grids/A): 1.917174 object centre (A): 15.36150 22.14850 4.270500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 292.1999 centred at (gu) : 90.93041 97.97812 88.78309 assigned negative charge : -290.2002 centred at (gu) : 91.29867 98.47524 88.54795 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 58093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17455 grid for indexing accessible points = 1.400000 m= 22268 mr = 39567 m= 3576 mr = 16997 m= 205 mr = 2356 m= 2 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 448 time to turn everything in is 0.4900000 number of dielectric boundary points 25135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14479 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) : 0.6390579 object centre at (A) : 15.36150 22.14850 4.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3204300E-02 8.2831951E-03 midg,1,midg; midg,igrid,midg 3.5544056E-02 -1.5472887E-02 1,midg,midg; igrid,midg,midg 1.1229679E-02 -4.8793852E-03 gauss-seidel spectral radius is 0.9985754 estimated iterations to convergence 210 setup time was (sec) 0.8400000 now iterating at: 11:04:55 rms-change max change #iterations 3.631705 191.7781 at 10iterations 1.670190 70.02505 at 20iterations 0.7694118 29.14152 at 30iterations 0.3542326 13.46153 at 40iterations 0.1633210 5.904137 at 50iterations 7.5401425E-02 2.586300 at 60iterations 3.4602515E-02 1.296135 at 70iterations 1.5889658E-02 0.5582962 at 80iterations 7.3349560E-03 0.3074665 at 90iterations 3.3751808E-03 0.1240120 at 100iterations 1.5535133E-03 5.0470352E-02 at 110iterations 7.1571063E-04 2.2918701E-02 at 120iterations finished qdiffx linear iterations at : 11:05:05 total time elapsed so far: 10.59000 # loops : 120 mean,max change (kT/e) : 7.1571063E-04 2.2918701E-02 energy calculations done at 10.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.77000 DelPhi exited at 11:05:05 10.774u 0.339s 0:11.48 96.6% 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 Dec 28 2011 at 11:05:05 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.875761 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): -4.544000 35.26700 ymin,ymax (A): -3.621000 47.91800 zmin,zma (A): -23.58300 32.12400 x,y,z range (A): 39.81100 51.53900 55.70700 scale (grids/A): 2.875761 object centre (A): 15.36150 22.14850 4.270500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 292.1999 centred at (gu) : 91.39561 101.9671 88.17461 assigned negative charge : -290.2002 centred at (gu) : 91.94801 102.7128 87.82196 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 134056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17455 grid for indexing accessible points = 1.400000 m= 69859 mr = 95705 m= 27208 mr = 57860 m= 6421 mr = 22716 m= 863 mr = 4896 m= 56 mr = 615 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.6900000 no. cavity mid-points inaccessible to solvent = 1530 time to turn everything in is 1.280000 number of dielectric boundary points 56638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 14702 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) : 1.917174 object centre at (A) : 15.36150 22.14850 4.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.150181 -2.5472425E-02 midg,1,midg; midg,igrid,midg 0.4045444 -0.2220232 1,midg,midg; igrid,midg,midg 7.8136548E-02 -2.8028049E-02 gauss-seidel spectral radius is 0.9992320 estimated iterations to convergence 285 setup time was (sec) 1.610000 now iterating at: 11:05:07 rms-change max change #iterations 8.562151 500.2088 at 10iterations 4.924082 123.0107 at 20iterations 2.809689 72.52022 at 30iterations 1.608859 37.80754 at 40iterations 0.9158194 25.20778 at 50iterations 0.5213453 12.44630 at 60iterations 0.2973692 6.317698 at 70iterations 0.1690091 3.558210 at 80iterations 9.5836677E-02 1.898647 at 90iterations 5.4542251E-02 1.111298 at 100iterations 3.0931449E-02 0.6603572 at 110iterations 1.7599041E-02 0.3869290 at 120iterations 9.9597890E-03 0.2041473 at 130iterations 5.6642829E-03 0.1151710 at 140iterations 3.2235312E-03 6.2870026E-02 at 150iterations 1.8282849E-03 4.1137695E-02 at 160iterations 1.0377434E-03 1.9916534E-02 at 170iterations 5.8853388E-04 1.1400223E-02 at 180iterations finished qdiffx linear iterations at : 11:05:18 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 5.8853388E-04 1.1400223E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 11:05:18 12.199u 0.359s 0:13.04 96.1% 0+0k 0+0io 0pf+0w