Mon Oct 10 14:43:13 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 Mon Oct 10 2011 at 14:43:13 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 !!! WARNING: GLN 230 has a net charge of 0.0260 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: 0.6251097 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): -23.11300 26.20900 ymin,ymax (A): -24.13500 32.81500 zmin,zma (A): -14.66300 36.97100 x,y,z range (A): 49.32200 56.95000 51.63400 scale (grids/A): 0.6251097 object centre (A): 1.548000 4.340001 11.15400 number of atom coordinates read : 2412 total number of charged atoms : 2253 net assigned charge : -2.973995 assigned positive charge : 355.4032 centred at (gu) : 90.70534 90.87922 89.88180 assigned negative charge : -358.3774 centred at (gu) : 90.89845 90.81939 89.91843 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6365 nv = 96 ne = 84 npr = 48408 no. pairs analyzed = 48408 no. exposed pairs = 3258 no. arc points = 22808 no. surface atoms = 1092 nbur = 1320 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3242 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2211 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2062958E-10 -5.1906057E-09 midg,1,midg; midg,igrid,midg -5.7761973E-09 1.8730948E-09 1,midg,midg; igrid,midg,midg 9.1430286E-09 -1.9568104E-08 gauss-seidel spectral radius is 0.9867360 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 14:43:14 rms-change max change #iterations 0.1241347 27.38087 at 10iterations 1.1518814E-02 1.913994 at 20iterations 1.0769247E-03 0.1685509 at 30iterations 1.0047564E-04 2.0336151E-02 at 40iterations 9.2881937E-06 1.6174316E-03 at 50iterations finished qdiffx linear iterations at : 14:43:18 total time elapsed so far: 4.970000 # loops : 50 mean,max change (kT/e) : 9.2881937E-06 1.6174316E-03 energy calculations done at 4.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 14:43:19 5.139u 0.468s 0:05.94 94.1% 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 Mon Oct 10 2011 at 14:43:19 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 !!! WARNING: GLN 230 has a net charge of 0.0260 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: 1.875329 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): -23.11300 26.20900 ymin,ymax (A): -24.13500 32.81500 zmin,zma (A): -14.66300 36.97100 x,y,z range (A): 49.32200 56.95000 51.63400 scale (grids/A): 1.875329 object centre (A): 1.548000 4.340001 11.15400 number of atom coordinates read : 2412 total number of charged atoms : 2253 net assigned charge : -2.973995 assigned positive charge : 355.4032 centred at (gu) : 92.11574 92.63717 89.64500 assigned negative charge : -358.3774 centred at (gu) : 92.69505 92.45801 89.75497 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22808 grid for indexing accessible points = 1.400000 m= 22961 mr = 46359 m= 3081 mr = 15945 m= 149 mr = 1541 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31594 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17713 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) : 0.6251097 object centre at (A) : 1.548000 4.340001 11.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7212184E-03 -1.3844230E-02 midg,1,midg; midg,igrid,midg 4.5364997E-03 -6.4845327E-03 1,midg,midg; igrid,midg,midg 5.6563010E-03 -2.9327329E-02 gauss-seidel spectral radius is 0.9985811 estimated iterations to convergence 210 setup time was (sec) 0.9200000 now iterating at: 14:43:28 rms-change max change #iterations 3.916344 182.1747 at 10iterations 1.795725 83.10246 at 20iterations 0.8261850 30.20670 at 30iterations 0.3797216 12.56059 at 40iterations 0.1749936 6.133900 at 50iterations 8.0496505E-02 3.021881 at 60iterations 3.7169311E-02 1.473864 at 70iterations 1.7124197E-02 0.5718479 at 80iterations 7.8786593E-03 0.2664113 at 90iterations 3.6272502E-03 0.1184235 at 100iterations 1.6743990E-03 5.0691128E-02 at 110iterations 7.7028631E-04 2.5957108E-02 at 120iterations finished qdiffx linear iterations at : 14:43:39 total time elapsed so far: 12.16000 # loops : 120 mean,max change (kT/e) : 7.7028631E-04 2.5957108E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 14:43:40 12.327u 0.608s 0:21.03 61.4% 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 Mon Oct 10 2011 at 14:43:40 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 !!! WARNING: GLN 230 has a net charge of 0.0260 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: 2.812994 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): -23.11300 26.20900 ymin,ymax (A): -24.13500 32.81500 zmin,zma (A): -14.66300 36.97100 x,y,z range (A): 49.32200 56.95000 51.63400 scale (grids/A): 2.812994 object centre (A): 1.548000 4.340001 11.15400 number of atom coordinates read : 2412 total number of charged atoms : 2253 net assigned charge : -2.973995 assigned positive charge : 355.4032 centred at (gu) : 93.17352 93.95568 89.46751 assigned negative charge : -358.3774 centred at (gu) : 94.04251 93.68695 89.63232 start vw surface at 0.1000000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 160057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22808 grid for indexing accessible points = 1.400000 m= 76486 mr = 113057 m= 24729 mr = 60459 m= 5154 mr = 18619 m= 594 mr = 3397 m= 28 mr = 323 m= 0 mr = 11 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 71182 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 18018 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) : 1.875329 object centre at (A) : 1.548000 4.340001 11.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8399404E-02 -0.2347939 midg,1,midg; midg,igrid,midg 0.1204584 -0.1140308 1,midg,midg; igrid,midg,midg 1.9477865E-02 -0.3193137 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 1.840000 now iterating at: 14:43:42 rms-change max change #iterations 9.445147 349.9035 at 10iterations 5.573344 158.4111 at 20iterations 3.263908 83.93260 at 30iterations 1.892122 42.66360 at 40iterations 1.094536 24.53806 at 50iterations 0.6322166 13.47844 at 60iterations 0.3643712 8.131867 at 70iterations 0.2099901 4.692183 at 80iterations 0.1202911 2.626666 at 90iterations 6.9290325E-02 1.521129 at 100iterations 3.9697956E-02 0.8385534 at 110iterations 2.2812305E-02 0.4543915 at 120iterations 1.3077624E-02 0.2558446 at 130iterations 7.4787475E-03 0.1500854 at 140iterations 4.2877905E-03 8.5363388E-02 at 150iterations 2.4490457E-03 4.4334412E-02 at 160iterations 1.4055341E-03 2.7916431E-02 at 170iterations 8.0434524E-04 1.4993668E-02 at 180iterations finished qdiffx linear iterations at : 14:44:01 total time elapsed so far: 20.30000 # loops : 180 mean,max change (kT/e) : 8.0434524E-04 1.4993668E-02 energy calculations done at 20.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.47000 DelPhi exited at 14:44:02 20.476u 0.571s 0:21.50 97.8% 0+0k 0+0io 0pf+0w