Tue Oct 11 08:07:52 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 08:07:52 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1017 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8889554 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): -5.156000 34.89100 ymin,ymax (A): -0.2990000 36.85300 zmin,zma (A): 4.221000 37.45300 x,y,z range (A): 40.04700 37.15200 33.23200 scale (grids/A): 0.8889554 object centre (A): 14.86750 18.27700 20.83700 number of atom coordinates read : 1017 total number of charged atoms : 944 net assigned charge : 1.500001 assigned positive charge : 148.3961 centred at (gu) : 90.81000 88.04604 89.78281 assigned negative charge : -146.8961 centred at (gu) : 90.77643 88.31023 89.72312 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5649 nv = 96 ne = 84 npr = 20197 no. pairs analyzed = 20197 no. exposed pairs = 1337 no. arc points = 9841 no. surface atoms = 456 nbur = 561 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 3002 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 3.9999999E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 3004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 482 ## 45 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4957 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2553236E-09 6.8381001E-07 midg,1,midg; midg,igrid,midg 2.5740155E-06 -8.8002548E-07 1,midg,midg; igrid,midg,midg 1.4685136E-07 6.3101709E-07 gauss-seidel spectral radius is 0.9932739 estimated iterations to convergence 98 setup time was (sec) 0.3100000 now iterating at: 08:07:52 rms-change max change #iterations 0.3171886 57.01659 at 10iterations 5.8835708E-02 8.294117 at 20iterations 1.0795108E-02 1.452339 at 30iterations 1.9987186E-03 0.2706819 at 40iterations 3.6921163E-04 6.3244343E-02 at 50iterations finished qdiffx linear iterations at : 08:07:55 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 3.6921163E-04 6.3244343E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 08:07:56 3.315u 0.163s 0:03.75 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 Tue Oct 11 2011 at 08:07:56 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1017 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.666866 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): -5.156000 34.89100 ymin,ymax (A): -0.2990000 36.85300 zmin,zma (A): 4.221000 37.45300 x,y,z range (A): 40.04700 37.15200 33.23200 scale (grids/A): 2.666866 object centre (A): 14.86750 18.27700 20.83700 number of atom coordinates read : 1017 total number of charged atoms : 944 net assigned charge : 1.500001 assigned positive charge : 148.3961 centred at (gu) : 92.42995 84.13807 89.34866 assigned negative charge : -146.8961 centred at (gu) : 92.32930 84.93070 89.16947 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 58211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 9841 grid for indexing accessible points = 1.400000 m= 23629 mr = 38850 m= 5818 mr = 17758 m= 786 mr = 3957 m= 46 mr = 447 m= 3 mr = 21 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 0.3200000 number of dielectric boundary points 27460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7552 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) : 0.8889554 object centre at (A) : 14.86750 18.27700 20.83700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8393777E-02 4.2183600E-02 midg,1,midg; midg,igrid,midg 6.0788762E-02 -4.9720902E-02 1,midg,midg; igrid,midg,midg -1.4659618E-02 6.8538718E-02 gauss-seidel spectral radius is 0.9991018 estimated iterations to convergence 264 setup time was (sec) 0.5200000 now iterating at: 08:07:56 rms-change max change #iterations 4.543905 250.5461 at 10iterations 2.466205 122.2402 at 20iterations 1.328913 42.57438 at 30iterations 0.7151269 22.16116 at 40iterations 0.3883295 12.18068 at 50iterations 0.2086666 6.677792 at 60iterations 0.1128819 3.597839 at 70iterations 6.0744327E-02 1.769279 at 80iterations 3.2783087E-02 1.108807 at 90iterations 1.7686645E-02 0.5368042 at 100iterations 9.5240381E-03 0.2995605 at 110iterations 5.1485188E-03 0.1446285 at 120iterations finished qdiffx linear iterations at : 08:08:03 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 5.1485188E-03 0.1446285 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 08:08:04 7.717u 0.200s 0:08.35 94.7% 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 Tue Oct 11 2011 at 08:08:04 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1017 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 4.000299 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): -5.156000 34.89100 ymin,ymax (A): -0.2990000 36.85300 zmin,zma (A): 4.221000 37.45300 x,y,z range (A): 40.04700 37.15200 33.23200 scale (grids/A): 4.000299 object centre (A): 14.86750 18.27700 20.83700 number of atom coordinates read : 1017 total number of charged atoms : 944 net assigned charge : 1.500001 assigned positive charge : 148.3961 centred at (gu) : 93.64484 81.20718 89.02298 assigned negative charge : -146.8961 centred at (gu) : 93.49403 82.39603 88.75423 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 133372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 9841 grid for indexing accessible points = 1.400000 m= 70474 mr = 93127 m= 32494 mr = 58071 m= 11386 mr = 26725 m= 2963 mr = 8944 m= 603 mr = 2174 m= 77 mr = 465 m= 4 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 61831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 7552 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) : 2.666866 object centre at (A) : 14.86750 18.27700 20.83700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2144814 0.2857819 midg,1,midg; midg,igrid,midg 0.4791264 -0.2573862 1,midg,midg; igrid,midg,midg -0.1324072 0.4931296 gauss-seidel spectral radius is 0.9993476 estimated iterations to convergence 309 setup time was (sec) 1.210000 now iterating at: 08:08:06 rms-change max change #iterations 9.259445 505.5181 at 10iterations 5.515253 156.2175 at 20iterations 3.282199 70.78763 at 30iterations 1.947565 36.39083 at 40iterations 1.155804 23.72371 at 50iterations 0.6850214 12.86029 at 60iterations 0.4073068 8.030178 at 70iterations 0.2422244 4.511154 at 80iterations 0.1434096 2.589081 at 90iterations 8.4992826E-02 1.706833 at 100iterations 5.0483044E-02 0.9432287 at 110iterations 2.9907236E-02 0.5453340 at 120iterations 1.7746748E-02 0.3280756 at 130iterations 1.0510653E-02 0.1916428 at 140iterations 6.2555955E-03 0.1148481 at 150iterations 3.7116974E-03 6.4415932E-02 at 160iterations 2.2076266E-03 3.6954641E-02 at 170iterations 1.3053922E-03 2.3636341E-02 at 180iterations finished qdiffx linear iterations at : 08:08:17 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 1.3053922E-03 2.3636341E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 08:08:17 12.454u 0.205s 0:12.96 97.6% 0+0k 0+0io 0pf+0w