Thu Jan 19 13:34:01 PST 2012 #!/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 Thu Jan 19 2012 at 13:34:01 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: 358 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6700 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LEU 263 has a net charge of -0.0260 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1108 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4645215 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): -3.603000 73.03500 ymin,ymax (A): -83.10900 -16.02400 zmin,zma (A): -28.12000 45.35500 x,y,z range (A): 76.63800 67.08500 73.47501 scale (grids/A): 0.4645215 object centre (A): 34.71600 -49.56650 8.617502 number of atom coordinates read : 6700 total number of charged atoms : 6530 net assigned charge : -4.608946 assigned positive charge : 1015.049 centred at (gu) : 90.13627 88.75231 89.67352 assigned negative charge : -1019.667 centred at (gu) : 90.21663 88.73959 89.63708 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8983 nv = 96 ne = 84 npr = 133607 no. pairs analyzed = 133607 no. exposed pairs = 8815 no. arc points = 59653 no. surface atoms = 2933 nbur = 3767 mkacc time = 0.2300000 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 = 1.820000 m= 275 mr = 4422 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5404 ## 973 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 12197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4395227E-11 7.9075904E-12 midg,1,midg; midg,igrid,midg -1.7267949E-11 -9.5269528E-13 1,midg,midg; igrid,midg,midg 2.5986827E-11 -4.2824508E-11 gauss-seidel spectral radius is 0.9764629 estimated iterations to convergence 54 setup time was (sec) 0.6500000 now iterating at: 13:34:03 rms-change max change #iterations 4.7277570E-02 6.981863 at 10iterations 3.1660954E-03 0.4810419 at 20iterations 1.1968551E-03 0.1962490 at 30iterations 5.5700715E-04 9.4132423E-02 at 40iterations 2.5922430E-04 4.4309616E-02 at 50iterations finished qdiffx linear iterations at : 13:34:10 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 2.5922430E-04 4.4309616E-02 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.860000 DelPhi exited at 13:34:10 3.865u 0.218s 0:09.73 41.8% 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 Thu Jan 19 2012 at 13:34:11 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: 358 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6700 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LEU 263 has a net charge of -0.0260 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1108 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.393565 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): -3.603000 73.03500 ymin,ymax (A): -83.10900 -16.02400 zmin,zma (A): -28.12000 45.35500 x,y,z range (A): 76.63800 67.08500 73.47501 scale (grids/A): 1.393565 object centre (A): 34.71600 -49.56650 8.617502 number of atom coordinates read : 6700 total number of charged atoms : 6530 net assigned charge : -4.608946 assigned positive charge : 1015.049 centred at (gu) : 90.40707 86.25508 89.01839 assigned negative charge : -1019.667 centred at (gu) : 90.64949 86.21844 88.91099 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 103871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59653 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 27082 mr = 70165 m= 1712 mr = 16706 m= 25 mr = 550 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 766 time to turn everything in is 0.5200000 number of dielectric boundary points 45269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 897 ## 22 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 47172 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) : 0.4645215 object centre at (A) : 34.71600 -49.56650 8.617502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0421578E-03 1.2471384E-02 midg,1,midg; midg,igrid,midg -7.6757424E-04 -5.5126293E-04 1,midg,midg; igrid,midg,midg 2.8487975E-03 -1.9686580E-02 gauss-seidel spectral radius is 0.9978481 estimated iterations to convergence 172 setup time was (sec) 0.7600000 now iterating at: 13:34:13 rms-change max change #iterations 3.750572 127.0957 at 10iterations 1.449093 45.35342 at 20iterations 0.5588391 17.07963 at 30iterations 0.2162823 6.698629 at 40iterations 8.3512537E-02 2.967883 at 50iterations 3.2443590E-02 1.072426 at 60iterations 1.2746481E-02 0.4292517 at 70iterations 5.1335581E-03 0.1488686 at 80iterations 2.2729209E-03 8.6418152E-02 at 90iterations 1.2009483E-03 4.5936584E-02 at 100iterations 7.7116513E-04 2.7681351E-02 at 110iterations 5.5202970E-04 1.8287659E-02 at 120iterations finished qdiffx linear iterations at : 13:34:28 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 5.5202970E-04 1.8287659E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 13:34:29 8.788u 0.232s 0:18.59 48.4% 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 Thu Jan 19 2012 at 13:34:29 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: 358 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6700 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LEU 263 has a net charge of -0.0260 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1108 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.090347 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): -3.603000 73.03500 ymin,ymax (A): -83.10900 -16.02400 zmin,zma (A): -28.12000 45.35500 x,y,z range (A): 76.63800 67.08500 73.47501 scale (grids/A): 2.090347 object centre (A): 34.71600 -49.56650 8.617502 number of atom coordinates read : 6700 total number of charged atoms : 6530 net assigned charge : -4.608946 assigned positive charge : 1015.049 centred at (gu) : 90.60992 84.38211 88.52738 assigned negative charge : -1019.667 centred at (gu) : 90.97412 84.32759 88.36650 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 243196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59653 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 101381 mr = 174174 m= 21414 mr = 76541 m= 2058 mr = 14118 m= 68 mr = 954 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 2666 time to turn everything in is 1.270000 number of dielectric boundary points 102320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 51860 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) : 1.393565 object centre at (A) : 34.71600 -49.56650 8.617502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3051094 0.4045048 midg,1,midg; midg,igrid,midg -1.6603753E-02 -1.1375126E-02 1,midg,midg; igrid,midg,midg 0.1558490 -0.3286041 gauss-seidel spectral radius is 0.9991222 estimated iterations to convergence 267 setup time was (sec) 1.600000 now iterating at: 13:34:33 rms-change max change #iterations 10.77830 285.8121 at 10iterations 6.079662 144.6259 at 20iterations 3.415049 74.97650 at 30iterations 1.909611 40.44514 at 40iterations 1.062294 23.01036 at 50iterations 0.5879735 12.16549 at 60iterations 0.3252114 6.133150 at 70iterations 0.1799610 3.383755 at 80iterations 9.9057332E-02 2.079666 at 90iterations 5.4462988E-02 1.042847 at 100iterations 2.9935781E-02 0.6060638 at 110iterations 1.6476853E-02 0.3071213 at 120iterations 9.0557802E-03 0.1730537 at 130iterations 4.9948664E-03 8.5905075E-02 at 140iterations 2.7658439E-03 4.9610138E-02 at 150iterations 1.5499118E-03 2.9909134E-02 at 160iterations 8.9162344E-04 1.7372131E-02 at 170iterations 5.3543074E-04 1.0593414E-02 at 180iterations finished qdiffx linear iterations at : 13:34:51 total time elapsed so far: 14.39000 # loops : 180 mean,max change (kT/e) : 5.3543074E-04 1.0593414E-02 energy calculations done at 14.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.54000 DelPhi exited at 13:34:52 14.541u 0.286s 0:22.68 65.3% 0+0k 0+0io 0pf+0w