Tue Oct 11 06:48:41 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 06:48:41 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 0.5466327 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): -19.83100 45.29500 ymin,ymax (A): 21.51400 78.67300 zmin,zma (A): -72.22100 -24.67700 x,y,z range (A): 65.12600 57.15900 47.54400 scale (grids/A): 0.5466327 object centre (A): 12.73200 50.09350 -48.44900 number of atom coordinates read : 2972 total number of charged atoms : 2826 net assigned charge : -3.054993 assigned positive charge : 434.3376 centred at (gu) : 89.33838 89.72133 90.47412 assigned negative charge : -437.3932 centred at (gu) : 89.31141 89.85181 90.46730 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5766 nv = 96 ne = 84 npr = 61030 no. pairs analyzed = 61030 no. exposed pairs = 3709 no. arc points = 25940 no. surface atoms = 1255 nbur = 1717 mkacc time = 0.1000000 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 = 1.568000 m= 229 mr = 3050 m= 0 mr = 13 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2637 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1568333E-10 -1.6833064E-10 midg,1,midg; midg,igrid,midg 7.1286049E-10 -1.0120553E-09 1,midg,midg; igrid,midg,midg -4.4429699E-10 -1.4853454E-11 gauss-seidel spectral radius is 0.9827470 estimated iterations to convergence 63 setup time was (sec) 0.4000000 now iterating at: 06:48:42 rms-change max change #iterations 7.3111102E-02 14.47640 at 10iterations 4.8754849E-03 0.8830576 at 20iterations 3.3726305E-04 5.2986145E-02 at 30iterations 2.4597099E-05 5.0430298E-03 at 40iterations 2.3414721E-06 4.6491623E-04 at 50iterations finished qdiffx linear iterations at : 06:48:45 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.3414721E-06 4.6491623E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 06:48:45 3.421u 0.173s 0:03.89 92.2% 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 06:48:45 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 1.639898 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): -19.83100 45.29500 ymin,ymax (A): 21.51400 78.67300 zmin,zma (A): -72.22100 -24.67700 x,y,z range (A): 65.12600 57.15900 47.54400 scale (grids/A): 1.639898 object centre (A): 12.73200 50.09350 -48.44900 number of atom coordinates read : 2972 total number of charged atoms : 2826 net assigned charge : -3.054993 assigned positive charge : 434.3376 centred at (gu) : 88.01475 89.16325 91.42209 assigned negative charge : -437.3932 centred at (gu) : 87.93401 89.55511 91.40137 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25940 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20208 mr = 43416 m= 2086 mr = 14322 m= 44 mr = 1129 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 321 time to turn everything in is 0.3100000 number of dielectric boundary points 27356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 21701 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) : 0.5466327 object centre at (A) : 12.73200 50.09350 -48.44900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5932562E-03 8.0870371E-03 midg,1,midg; midg,igrid,midg -5.4558045E-03 3.0694953E-03 1,midg,midg; igrid,midg,midg -6.0343561E-03 -3.0238055E-02 gauss-seidel spectral radius is 0.9982044 estimated iterations to convergence 187 setup time was (sec) 0.5300000 now iterating at: 06:48:46 rms-change max change #iterations 3.316389 189.1646 at 10iterations 1.387255 51.16824 at 20iterations 0.5815393 23.10789 at 30iterations 0.2440932 8.764303 at 40iterations 0.1022188 3.602730 at 50iterations 4.2853661E-02 1.642171 at 60iterations 1.7965352E-02 0.6491623 at 70iterations 7.5277942E-03 0.2725576 at 80iterations 3.1659992E-03 0.1078186 at 90iterations 1.3236592E-03 5.0759315E-02 at 100iterations 5.5768137E-04 2.2094727E-02 at 110iterations 2.3409874E-04 8.8977814E-03 at 120iterations finished qdiffx linear iterations at : 06:48:53 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.3409874E-04 8.8977814E-03 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 06:48:54 7.697u 0.209s 0:08.43 93.5% 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 06:48:54 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 2.459847 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): -19.83100 45.29500 ymin,ymax (A): 21.51400 78.67300 zmin,zma (A): -72.22100 -24.67700 x,y,z range (A): 65.12600 57.15900 47.54400 scale (grids/A): 2.459847 object centre (A): 12.73200 50.09350 -48.44900 number of atom coordinates read : 2972 total number of charged atoms : 2826 net assigned charge : -3.054993 assigned positive charge : 434.3376 centred at (gu) : 87.02202 88.74474 92.13298 assigned negative charge : -437.3932 centred at (gu) : 86.90082 89.33259 92.10198 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 148329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25940 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 69356 mr = 106040 m= 20283 mr = 55665 m= 3252 mr = 15678 m= 233 mr = 2325 m= 7 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1022 time to turn everything in is 0.7800000 number of dielectric boundary points 61628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 22588 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) : 1.639898 object centre at (A) : 12.73200 50.09350 -48.44900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9494508E-02 0.1499032 midg,1,midg; midg,igrid,midg -7.6821111E-02 5.8731243E-02 1,midg,midg; igrid,midg,midg -9.7277127E-02 -0.8219093 gauss-seidel spectral radius is 0.9991463 estimated iterations to convergence 270 setup time was (sec) 1.020000 now iterating at: 06:48:55 rms-change max change #iterations 8.544119 262.9203 at 10iterations 4.789631 150.0826 at 20iterations 2.675768 66.95415 at 30iterations 1.489185 39.85912 at 40iterations 0.8291180 17.67601 at 50iterations 0.4582228 10.58167 at 60iterations 0.2533014 6.748558 at 70iterations 0.1400102 3.042994 at 80iterations 7.7374250E-02 1.703121 at 90iterations 4.2567238E-02 0.9519348 at 100iterations 2.3475431E-02 0.4834824 at 110iterations 1.2941271E-02 0.2731819 at 120iterations 7.1196058E-03 0.1556625 at 130iterations 3.9326036E-03 7.8093529E-02 at 140iterations 2.1634244E-03 4.3499947E-02 at 150iterations 1.1940462E-03 2.4685860E-02 at 160iterations 6.5607537E-04 1.3584137E-02 at 170iterations 3.6161521E-04 7.7009201E-03 at 180iterations finished qdiffx linear iterations at : 06:49:06 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 3.6161521E-04 7.7009201E-03 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 06:49:07 12.284u 0.208s 0:12.78 97.6% 0+0k 0+0io 0pf+0w