Sun Oct 9 01:49:10 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+sph.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 = amb.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 01:49:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 0.6638942 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): -27.12000 26.50300 ymin,ymax (A): 8.695000 52.62100 zmin,zma (A): -11.67000 41.78600 x,y,z range (A): 53.62300 43.92600 53.45600 scale (grids/A): 0.6638942 object centre (A): -0.3085003 30.65800 15.05800 number of atom coordinates read : 2318 total number of charged atoms : 2183 net assigned charge : 10.50002 assigned positive charge : 336.4425 centred at (gu) : 90.50143 90.83960 91.20798 assigned negative charge : -325.9432 centred at (gu) : 90.53644 90.72913 91.17522 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7090 nv = 96 ne = 84 npr = 46372 no. pairs analyzed = 46372 no. exposed pairs = 3104 no. arc points = 22822 no. surface atoms = 1022 nbur = 1296 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 420 mr = 3672 m= 0 mr = 47 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3200000 number of dielectric boundary points 3791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2102 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8093 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8435882E-08 4.5140286E-08 midg,1,midg; midg,igrid,midg 7.6909243E-09 5.8627855E-08 1,midg,midg; igrid,midg,midg 3.2313697E-08 2.5289932E-08 gauss-seidel spectral radius is 0.9882247 estimated iterations to convergence 75 setup time was (sec) 0.5900000 now iterating at: 01:49:11 rms-change max change #iterations 0.1563351 26.35540 at 10iterations 1.6756579E-02 2.555855 at 20iterations 1.7765752E-03 0.2517834 at 30iterations 2.0029285E-04 3.2646179E-02 at 40iterations 2.3406872E-05 3.4008026E-03 at 50iterations finished qdiffx linear iterations at : 01:49:14 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 2.3406872E-05 3.4008026E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 01:49:14 4.040u 0.258s 0:04.56 94.0% 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 01:49:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 1.991683 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): -27.12000 26.50300 ymin,ymax (A): 8.695000 52.62100 zmin,zma (A): -11.67000 41.78600 x,y,z range (A): 53.62300 43.92600 53.45600 scale (grids/A): 1.991683 object centre (A): -0.3085003 30.65800 15.05800 number of atom coordinates read : 2318 total number of charged atoms : 2183 net assigned charge : 10.50002 assigned positive charge : 336.4425 centred at (gu) : 91.50377 92.51857 93.62351 assigned negative charge : -325.9432 centred at (gu) : 91.60956 92.18744 93.52565 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22822 grid for indexing accessible points = 1.400000 m= 27983 mr = 50254 m= 5103 mr = 20136 m= 428 mr = 3270 m= 14 mr = 177 m= 0 mr = 3 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 17281 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) : 0.6638942 object centre at (A) : -0.3085003 30.65800 15.05800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8772901E-02 3.7062280E-02 midg,1,midg; midg,igrid,midg -1.1051572E-02 3.2019354E-02 1,midg,midg; igrid,midg,midg 5.9876803E-02 7.3254734E-02 gauss-seidel spectral radius is 0.9987323 estimated iterations to convergence 222 setup time was (sec) 0.9900000 now iterating at: 01:49:16 rms-change max change #iterations 4.188688 181.1285 at 10iterations 2.016534 76.97974 at 20iterations 0.9639004 31.49719 at 30iterations 0.4642407 16.02808 at 40iterations 0.2223422 7.464215 at 50iterations 0.1068536 3.677229 at 60iterations 5.1391181E-02 1.549721 at 70iterations 2.4742462E-02 0.7769699 at 80iterations 1.1887517E-02 0.4065590 at 90iterations 5.7275952E-03 0.1755486 at 100iterations 2.7582012E-03 8.2452536E-02 at 110iterations 1.3249858E-03 4.0725708E-02 at 120iterations finished qdiffx linear iterations at : 01:49:24 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 1.3249858E-03 4.0725708E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 01:49:24 9.462u 0.283s 0:10.01 97.3% 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 01:49:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 2.987524 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): -27.12000 26.50300 ymin,ymax (A): 8.695000 52.62100 zmin,zma (A): -11.67000 41.78600 x,y,z range (A): 53.62300 43.92600 53.45600 scale (grids/A): 2.987524 object centre (A): -0.3085003 30.65800 15.05800 number of atom coordinates read : 2318 total number of charged atoms : 2183 net assigned charge : 10.50002 assigned positive charge : 336.4425 centred at (gu) : 92.25561 93.77791 95.43532 assigned negative charge : -325.9432 centred at (gu) : 92.41433 93.28114 95.28847 start vw surface at 0.1500000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 173517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22822 grid for indexing accessible points = 1.400000 m= 87979 mr = 121885 m= 33957 mr = 70557 m= 9505 mr = 27082 m= 1747 mr = 7266 m= 206 mr = 1196 m= 17 mr = 121 m= 0 mr = 9 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 78812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 17464 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) : 1.991683 object centre at (A) : -0.3085003 30.65800 15.05800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6487239 0.3783284 midg,1,midg; midg,igrid,midg -0.1256960 0.2844909 1,midg,midg; igrid,midg,midg 0.5607013 0.6564988 gauss-seidel spectral radius is 0.9992974 estimated iterations to convergence 298 setup time was (sec) 2.090000 now iterating at: 01:49:27 rms-change max change #iterations 9.883704 416.2339 at 10iterations 5.866839 137.5967 at 20iterations 3.471833 76.21127 at 30iterations 2.047326 39.90325 at 40iterations 1.203327 22.90275 at 50iterations 0.7077184 15.35857 at 60iterations 0.4144549 7.659073 at 70iterations 0.2421567 4.346577 at 80iterations 0.1418107 2.565758 at 90iterations 8.2758144E-02 1.545761 at 100iterations 4.8396800E-02 0.9173470 at 110iterations 2.8280338E-02 0.6132007 at 120iterations 1.6502840E-02 0.3125000 at 130iterations 9.6313050E-03 0.1848755 at 140iterations 5.6129098E-03 9.7013474E-02 at 150iterations 3.2817258E-03 6.0432434E-02 at 160iterations 1.9168120E-03 3.6531448E-02 at 170iterations 1.1221073E-03 2.0578384E-02 at 180iterations finished qdiffx linear iterations at : 01:49:41 total time elapsed so far: 15.77000 # loops : 180 mean,max change (kT/e) : 1.1221073E-03 2.0578384E-02 energy calculations done at 15.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.95000 DelPhi exited at 01:49:41 15.951u 0.314s 0:16.55 98.2% 0+0k 0+0io 0pf+0w