Tue Oct 11 05:15:55 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 05:15:55 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2190 !!! WARNING: SEP 172 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6912889 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): 19.86700 63.13800 ymin,ymax (A): -3.576000 33.45400 zmin,zma (A): 20.42700 71.92500 x,y,z range (A): 43.27100 37.03000 51.49800 scale (grids/A): 0.6912889 object centre (A): 41.50250 14.93900 46.17600 number of atom coordinates read : 2190 total number of charged atoms : 1900 net assigned charge : 7.025010 assigned positive charge : 307.8201 centred at (gu) : 90.06280 89.81841 89.47903 assigned negative charge : -300.7952 centred at (gu) : 90.25563 89.84108 89.48329 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6583 nv = 96 ne = 84 npr = 39290 no. pairs analyzed = 39290 no. exposed pairs = 2487 no. arc points = 17120 no. surface atoms = 846 nbur = 1344 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 3740 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1666 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7411 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6013263E-08 3.5122262E-08 midg,1,midg; midg,igrid,midg 4.9372119E-08 3.1607854E-08 1,midg,midg; igrid,midg,midg 1.0128925E-07 -2.5004693E-08 gauss-seidel spectral radius is 0.9890925 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 05:15:56 rms-change max change #iterations 0.1734371 25.56613 at 10iterations 2.0549877E-02 3.166580 at 20iterations 2.6342806E-03 0.3517227 at 30iterations 3.9023618E-04 5.7357788E-02 at 40iterations 8.7680630E-05 1.1322021E-02 at 50iterations finished qdiffx linear iterations at : 05:15:59 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 8.7680630E-05 1.1322021E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 05:15:59 3.387u 0.172s 0:03.86 91.9% 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 05:15:59 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2190 !!! WARNING: SEP 172 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.073867 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): 19.86700 63.13800 ymin,ymax (A): -3.576000 33.45400 zmin,zma (A): 20.42700 71.92500 x,y,z range (A): 43.27100 37.03000 51.49800 scale (grids/A): 2.073867 object centre (A): 41.50250 14.93900 46.17600 number of atom coordinates read : 2190 total number of charged atoms : 1900 net assigned charge : 7.025010 assigned positive charge : 307.8201 centred at (gu) : 90.18858 89.45544 88.43726 assigned negative charge : -300.7952 centred at (gu) : 90.76682 89.52324 88.45001 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70018 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17120 grid for indexing accessible points = 1.400000 m= 28030 mr = 49291 m= 5376 mr = 21238 m= 483 mr = 3626 m= 8 mr = 225 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 29535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15045 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) : 0.6912889 object centre at (A) : 41.50250 14.93900 46.17600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4592734E-02 3.2095447E-02 midg,1,midg; midg,igrid,midg 2.1832885E-02 1.2086049E-02 1,midg,midg; igrid,midg,midg 4.0468149E-02 1.1049127E-02 gauss-seidel spectral radius is 0.9987800 estimated iterations to convergence 227 setup time was (sec) 0.5800000 now iterating at: 05:16:00 rms-change max change #iterations 4.309724 208.5102 at 10iterations 2.115017 75.09148 at 20iterations 1.026506 38.66090 at 30iterations 0.5054337 15.78209 at 40iterations 0.2463273 7.976945 at 50iterations 0.1209258 3.778888 at 60iterations 5.9151795E-02 1.850750 at 70iterations 2.9013988E-02 0.9123898 at 80iterations 1.4172007E-02 0.4335608 at 90iterations 7.0180260E-03 0.2667276 at 100iterations 3.4652702E-03 0.1087270 at 110iterations 1.7382434E-03 5.6013107E-02 at 120iterations finished qdiffx linear iterations at : 05:16:07 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.7382434E-03 5.6013107E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 05:16:08 7.814u 0.197s 0:08.35 95.8% 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 05:16:08 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2190 !!! WARNING: SEP 172 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.110800 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): 19.86700 63.13800 ymin,ymax (A): -3.576000 33.45400 zmin,zma (A): 20.42700 71.92500 x,y,z range (A): 43.27100 37.03000 51.49800 scale (grids/A): 3.110800 object centre (A): 41.50250 14.93900 46.17600 number of atom coordinates read : 2190 total number of charged atoms : 1900 net assigned charge : 7.025010 assigned positive charge : 307.8201 centred at (gu) : 90.28291 89.18316 87.65593 assigned negative charge : -300.7952 centred at (gu) : 91.15022 89.28501 87.67509 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 161409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17120 grid for indexing accessible points = 1.400000 m= 87669 mr = 118830 m= 35539 mr = 72915 m= 10111 mr = 29217 m= 1926 mr = 7770 m= 201 mr = 1431 m= 1 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 66569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 15200 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) : 2.073867 object centre at (A) : 41.50250 14.93900 46.17600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3476733 0.2414138 midg,1,midg; midg,igrid,midg 0.1895983 9.7300135E-02 1,midg,midg; igrid,midg,midg 0.3344561 0.2641768 gauss-seidel spectral radius is 0.9992841 estimated iterations to convergence 295 setup time was (sec) 1.310000 now iterating at: 05:16:09 rms-change max change #iterations 9.829672 454.3983 at 10iterations 5.793342 126.3402 at 20iterations 3.405808 73.31198 at 30iterations 1.997667 39.80643 at 40iterations 1.167704 28.84394 at 50iterations 0.6817293 11.93829 at 60iterations 0.3983098 7.547591 at 70iterations 0.2325795 4.524647 at 80iterations 0.1356405 2.337315 at 90iterations 7.9031557E-02 1.428112 at 100iterations 4.6160992E-02 0.9283981 at 110iterations 2.7063534E-02 0.5645361 at 120iterations 1.5900444E-02 0.3300133 at 130iterations 9.4895214E-03 0.1889420 at 140iterations 5.7326476E-03 0.1147308 at 150iterations 3.5602718E-03 7.5016022E-02 at 160iterations 2.3158211E-03 4.6772003E-02 at 170iterations 1.5814326E-03 3.2718658E-02 at 180iterations finished qdiffx linear iterations at : 05:16:20 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 1.5814326E-03 3.2718658E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 05:16:21 12.681u 0.221s 0:13.18 97.8% 0+0k 0+0io 0pf+0w