Tue Oct 11 03:28:25 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 Tue Oct 11 2011 at 03:28:25 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 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: 0.6144817 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): -13.64200 44.29300 ymin,ymax (A): -1.110000 55.17000 zmin,zma (A): 33.54900 89.67000 x,y,z range (A): 57.93500 56.28000 56.12100 scale (grids/A): 0.6144817 object centre (A): 15.32550 27.03000 61.60950 number of atom coordinates read : 3122 total number of charged atoms : 2966 net assigned charge : -0.4999940 assigned positive charge : 472.9891 centred at (gu) : 89.54762 90.10876 91.33955 assigned negative charge : -473.4903 centred at (gu) : 89.60400 90.20956 91.11868 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7970 nv = 96 ne = 84 npr = 60964 no. pairs analyzed = 60964 no. exposed pairs = 4323 no. arc points = 29858 no. surface atoms = 1462 nbur = 1660 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 4019 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2917 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1967153E-08 1.9407830E-08 midg,1,midg; midg,igrid,midg 6.1598655E-09 -7.7732532E-09 1,midg,midg; igrid,midg,midg 3.6654830E-09 -4.0354129E-09 gauss-seidel spectral radius is 0.9863401 estimated iterations to convergence 70 setup time was (sec) 0.4100000 now iterating at: 03:28:26 rms-change max change #iterations 0.1339056 18.67483 at 10iterations 1.1887144E-02 1.883389 at 20iterations 1.0841229E-03 0.1666708 at 30iterations 1.0338071E-04 1.3981819E-02 at 40iterations 1.6378215E-05 2.9602051E-03 at 50iterations finished qdiffx linear iterations at : 03:28:29 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.6378215E-05 2.9602051E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:28:29 3.427u 0.178s 0:03.92 91.5% 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 Tue Oct 11 2011 at 03:28:29 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 # of charge parameter records: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 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: 1.843445 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): -13.64200 44.29300 ymin,ymax (A): -1.110000 55.17000 zmin,zma (A): 33.54900 89.67000 x,y,z range (A): 57.93500 56.28000 56.12100 scale (grids/A): 1.843445 object centre (A): 15.32550 27.03000 61.60950 number of atom coordinates read : 3122 total number of charged atoms : 2966 net assigned charge : -0.4999940 assigned positive charge : 472.9891 centred at (gu) : 88.64226 90.32556 94.01792 assigned negative charge : -473.4903 centred at (gu) : 88.81181 90.62842 93.35561 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29858 grid for indexing accessible points = 1.400000 m= 28932 mr = 57489 m= 3683 mr = 19716 m= 173 mr = 1905 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 248 time to turn everything in is 0.4200000 number of dielectric boundary points 39759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 23212 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) : 0.6144817 object centre at (A) : 15.32550 27.03000 61.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4110902E-02 5.1889215E-02 midg,1,midg; midg,igrid,midg 1.9209357E-02 8.6989924E-03 1,midg,midg; igrid,midg,midg 4.1422527E-03 -2.9090406E-02 gauss-seidel spectral radius is 0.9986075 estimated iterations to convergence 212 setup time was (sec) 0.6300000 now iterating at: 03:28:30 rms-change max change #iterations 4.464053 206.9534 at 10iterations 2.056905 64.17427 at 20iterations 0.9515164 32.76888 at 30iterations 0.4405104 14.12289 at 40iterations 0.2043196 6.246144 at 50iterations 9.5323868E-02 3.150692 at 60iterations 4.4084612E-02 1.423653 at 70iterations 2.0420229E-02 0.6148223 at 80iterations 9.4865626E-03 0.2974863 at 90iterations 4.4028712E-03 0.1469374 at 100iterations 2.0529830E-03 6.1874390E-02 at 110iterations 9.5100712E-04 3.2426834E-02 at 120iterations finished qdiffx linear iterations at : 03:28:37 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 9.5100712E-04 3.2426834E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 03:28:38 7.953u 0.208s 0:08.45 96.4% 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 Tue Oct 11 2011 at 03:28:38 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 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: 2.765168 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): -13.64200 44.29300 ymin,ymax (A): -1.110000 55.17000 zmin,zma (A): 33.54900 89.67000 x,y,z range (A): 57.93500 56.28000 56.12100 scale (grids/A): 2.765168 object centre (A): 15.32550 27.03000 61.60950 number of atom coordinates read : 3122 total number of charged atoms : 2966 net assigned charge : -0.4999940 assigned positive charge : 472.9891 centred at (gu) : 87.96327 90.48808 96.02674 assigned negative charge : -473.4903 centred at (gu) : 88.21762 90.94250 95.03326 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 199378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29858 grid for indexing accessible points = 1.400000 m= 95588 mr = 140348 m= 31047 mr = 75151 m= 6181 mr = 23264 m= 672 mr = 4050 m= 32 mr = 399 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 815 time to turn everything in is 1.070000 number of dielectric boundary points 89677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 23726 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) : 1.843445 object centre at (A) : 15.32550 27.03000 61.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6704375 0.3896831 midg,1,midg; midg,igrid,midg 0.1766349 9.9718675E-02 1,midg,midg; igrid,midg,midg 0.1446089 -0.2900235 gauss-seidel spectral radius is 0.9992710 estimated iterations to convergence 292 setup time was (sec) 1.320000 now iterating at: 03:28:39 rms-change max change #iterations 10.82883 308.6883 at 10iterations 6.470240 144.0899 at 20iterations 3.811652 74.59416 at 30iterations 2.235643 47.93010 at 40iterations 1.307210 25.05355 at 50iterations 0.7645269 15.47079 at 60iterations 0.4436951 8.317677 at 70iterations 0.2575982 4.967884 at 80iterations 0.1492555 2.681171 at 90iterations 8.6819761E-02 1.521757 at 100iterations 5.0170198E-02 0.8467407 at 110iterations 2.8997842E-02 0.5082703 at 120iterations 1.6790789E-02 0.3058329 at 130iterations 9.6993074E-03 0.1752501 at 140iterations 5.6116404E-03 9.6472681E-02 at 150iterations 3.2452031E-03 5.4380417E-02 at 160iterations 1.8716764E-03 3.3876181E-02 at 170iterations 1.0818174E-03 1.9142151E-02 at 180iterations finished qdiffx linear iterations at : 03:28:51 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 1.0818174E-03 1.9142151E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 03:28:51 13.106u 0.196s 0:13.74 96.7% 0+0k 0+0io 0pf+0w