Sun Oct 9 06:42:11 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 06:42:11 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: ASP 372 has a net charge of -2.0000 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: 0.5854396 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): -27.99100 32.81800 ymin,ymax (A): -0.8860000 57.69800 zmin,zma (A): -27.21600 29.08000 x,y,z range (A): 60.80900 58.58400 56.29600 scale (grids/A): 0.5854396 object centre (A): 2.413500 28.40600 0.9320002 number of atom coordinates read : 2463 total number of charged atoms : 2315 net assigned charge : -2.093984 assigned positive charge : 365.5451 centred at (gu) : 90.73087 89.44602 90.45930 assigned negative charge : -367.6397 centred at (gu) : 90.75689 89.33516 90.43462 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5827 nv = 96 ne = 84 npr = 47686 no. pairs analyzed = 47686 no. exposed pairs = 3607 no. arc points = 26816 no. surface atoms = 1211 nbur = 1252 mkacc time = 0.1300000 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 = 1.456000 m= 251 mr = 2642 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2756 ## 324 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7247 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6453723E-10 5.9341351E-12 midg,1,midg; midg,igrid,midg -3.3913659E-09 1.6182674E-09 1,midg,midg; igrid,midg,midg 2.2190012E-11 -1.3040679E-09 gauss-seidel spectral radius is 0.9849135 estimated iterations to convergence 67 setup time was (sec) 0.6500000 now iterating at: 06:42:12 rms-change max change #iterations 9.0737440E-02 23.21920 at 10iterations 7.2818385E-03 1.357155 at 20iterations 5.6892395E-04 9.0007782E-02 at 30iterations 4.4475284E-05 7.3556900E-03 at 40iterations 3.7024670E-06 5.8555603E-04 at 50iterations finished qdiffx linear iterations at : 06:42:15 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 3.7024670E-06 5.8555603E-04 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 06:42:16 4.242u 0.252s 0:04.80 93.5% 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 06:42:16 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: ASP 372 has a net charge of -2.0000 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: 1.756319 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): -27.99100 32.81800 ymin,ymax (A): -0.8860000 57.69800 zmin,zma (A): -27.21600 29.08000 x,y,z range (A): 60.80900 58.58400 56.29600 scale (grids/A): 1.756319 object centre (A): 2.413500 28.40600 0.9320002 number of atom coordinates read : 2463 total number of charged atoms : 2315 net assigned charge : -2.093984 assigned positive charge : 365.5451 centred at (gu) : 92.19209 88.33772 91.37770 assigned negative charge : -367.6397 centred at (gu) : 92.27055 88.00542 91.30362 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 62622 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26816 grid for indexing accessible points = 1.400000 m= 19416 mr = 38856 m= 2278 mr = 12733 m= 90 mr = 1129 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 127 time to turn everything in is 0.5700000 number of dielectric boundary points 31680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 259 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 18011 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) : 0.5854396 object centre at (A) : 2.413500 28.40600 0.9320002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7578335E-02 9.5419772E-03 midg,1,midg; midg,igrid,midg -3.3404898E-02 -1.4014512E-03 1,midg,midg; igrid,midg,midg -1.3111260E-02 6.3535883E-03 gauss-seidel spectral radius is 0.9984097 estimated iterations to convergence 199 setup time was (sec) 0.8900000 now iterating at: 06:42:17 rms-change max change #iterations 3.502360 152.4615 at 10iterations 1.525725 58.99285 at 20iterations 0.6695520 25.88188 at 30iterations 0.2928047 10.87226 at 40iterations 0.1293933 4.993753 at 50iterations 5.6621686E-02 2.024537 at 60iterations 2.4932832E-02 0.9932022 at 70iterations 1.0946454E-02 0.4010429 at 80iterations 4.8198258E-03 0.1756229 at 90iterations 2.1158967E-03 7.9177856E-02 at 100iterations 9.2960888E-04 3.5369396E-02 at 110iterations 4.1034067E-04 1.5726089E-02 at 120iterations finished qdiffx linear iterations at : 06:42:25 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 4.1034067E-04 1.5726089E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 06:42:26 9.501u 0.279s 0:10.10 96.7% 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 06:42:26 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: ASP 372 has a net charge of -2.0000 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: 2.634478 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): -27.99100 32.81800 ymin,ymax (A): -0.8860000 57.69800 zmin,zma (A): -27.21600 29.08000 x,y,z range (A): 60.80900 58.58400 56.29600 scale (grids/A): 2.634478 object centre (A): 2.413500 28.40600 0.9320002 number of atom coordinates read : 2463 total number of charged atoms : 2315 net assigned charge : -2.093984 assigned positive charge : 365.5451 centred at (gu) : 93.28802 87.50645 92.06639 assigned negative charge : -367.6397 centred at (gu) : 93.40573 87.00805 91.95544 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 144704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26816 grid for indexing accessible points = 1.400000 m= 65451 mr = 95559 m= 19618 mr = 49991 m= 3697 mr = 14354 m= 337 mr = 2374 m= 9 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 429 time to turn everything in is 1.270000 number of dielectric boundary points 71395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18506 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) : 1.756319 object centre at (A) : 2.413500 28.40600 0.9320002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3644602 0.2675626 midg,1,midg; midg,igrid,midg -0.4766130 -3.0793624E-03 1,midg,midg; igrid,midg,midg -0.2718637 0.1860766 gauss-seidel spectral radius is 0.9992099 estimated iterations to convergence 281 setup time was (sec) 1.620000 now iterating at: 06:42:28 rms-change max change #iterations 8.721622 291.6019 at 10iterations 5.069547 157.0831 at 20iterations 2.913278 95.12656 at 30iterations 1.667890 43.09460 at 40iterations 0.9508318 24.26091 at 50iterations 0.5416411 13.93778 at 60iterations 0.3071208 8.202783 at 70iterations 0.1747027 4.134887 at 80iterations 9.8754242E-02 2.231960 at 90iterations 5.5699758E-02 1.189543 at 100iterations 3.1540532E-02 0.7570801 at 110iterations 1.7763475E-02 0.3751087 at 120iterations 1.0044642E-02 0.2102165 at 130iterations 5.6569907E-03 0.1235657 at 140iterations 3.1914574E-03 6.7348480E-02 at 150iterations 1.7997897E-03 3.6033630E-02 at 160iterations 1.0148854E-03 2.1289825E-02 at 170iterations 5.7006086E-04 1.1442184E-02 at 180iterations finished qdiffx linear iterations at : 06:42:41 total time elapsed so far: 15.08000 # loops : 180 mean,max change (kT/e) : 5.7006086E-04 1.1442184E-02 energy calculations done at 15.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.25000 DelPhi exited at 06:42:42 15.256u 0.283s 0:15.81 98.2% 0+0k 0+0io 0pf+0w