Sat Oct 15 11:25:55 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+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 Sat Oct 15 2011 at 11:25:55 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 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: 0.6038504 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): -61.40300 -2.448000 ymin,ymax (A): -24.91000 27.20800 zmin,zma (A): -10.10500 43.48100 x,y,z range (A): 58.95500 52.11800 53.58600 scale (grids/A): 0.6038504 object centre (A): -31.92550 1.149000 16.68800 number of atom coordinates read : 3016 total number of charged atoms : 2872 net assigned charge : 1.000014 assigned positive charge : 449.5391 centred at (gu) : 91.69576 89.96836 90.08066 assigned negative charge : -448.5404 centred at (gu) : 91.75428 89.95280 90.07333 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7288 nv = 96 ne = 84 npr = 62089 no. pairs analyzed = 62089 no. exposed pairs = 3474 no. arc points = 24162 no. surface atoms = 1180 nbur = 1836 mkacc time = 0.1100000 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 = 1.456000 m= 324 mr = 4148 m= 0 mr = 36 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2300000 number of dielectric boundary points 3428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2477 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8687261E-10 8.9946722E-10 midg,1,midg; midg,igrid,midg -2.0265856E-10 1.2632591E-09 1,midg,midg; igrid,midg,midg 2.2419842E-09 -3.3543710E-09 gauss-seidel spectral radius is 0.9858348 estimated iterations to convergence 69 setup time was (sec) 0.4800000 now iterating at: 11:25:57 rms-change max change #iterations 0.1225608 18.27963 at 10iterations 1.0902412E-02 1.510526 at 20iterations 1.0614825E-03 0.1492195 at 30iterations 1.3404977E-04 1.8585205E-02 at 40iterations 2.2715150E-05 2.9182434E-03 at 50iterations finished qdiffx linear iterations at : 11:26:02 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 2.2715150E-05 2.9182434E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 11:26:03 4.239u 0.307s 0:08.30 54.5% 0+0k 0+0io 3pf+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 Sat Oct 15 2011 at 11:26:03 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 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: 1.811551 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): -61.40300 -2.448000 ymin,ymax (A): -24.91000 27.20800 zmin,zma (A): -10.10500 43.48100 x,y,z range (A): 58.95500 52.11800 53.58600 scale (grids/A): 1.811551 object centre (A): -31.92550 1.149000 16.68800 number of atom coordinates read : 3016 total number of charged atoms : 2872 net assigned charge : 1.000014 assigned positive charge : 449.5391 centred at (gu) : 95.08614 89.90430 90.24150 assigned negative charge : -448.5404 centred at (gu) : 95.26260 89.85822 90.21980 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24162 grid for indexing accessible points = 1.400000 m= 27901 mr = 57609 m= 3546 mr = 20485 m= 141 mr = 2122 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2624 time to turn everything in is 0.4300000 number of dielectric boundary points 31712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 22453 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) : 0.6038504 object centre at (A) : -31.92550 1.149000 16.68800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3430029E-03 -1.9623918E-02 midg,1,midg; midg,igrid,midg 2.2006019E-03 1.1716965E-02 1,midg,midg; igrid,midg,midg 2.8278304E-02 2.4982458E-03 gauss-seidel spectral radius is 0.9985309 estimated iterations to convergence 207 setup time was (sec) 0.7100000 now iterating at: 11:26:04 rms-change max change #iterations 4.150659 153.3531 at 10iterations 1.885625 60.41054 at 20iterations 0.8611409 27.63221 at 30iterations 0.3907636 12.03668 at 40iterations 0.1787166 5.479370 at 50iterations 8.1843585E-02 2.792431 at 60iterations 3.7207596E-02 1.100821 at 70iterations 1.7052310E-02 0.4975500 at 80iterations 7.7951965E-03 0.2434769 at 90iterations 3.5846566E-03 0.1297579 at 100iterations 1.6529149E-03 4.9771309E-02 at 110iterations 7.7027373E-04 2.6351929E-02 at 120iterations finished qdiffx linear iterations at : 11:26:14 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 7.7027373E-04 2.6351929E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 11:26:15 9.557u 0.318s 0:11.35 86.8% 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 Sat Oct 15 2011 at 11:26:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 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: 2.717327 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): -61.40300 -2.448000 ymin,ymax (A): -24.91000 27.20800 zmin,zma (A): -10.10500 43.48100 x,y,z range (A): 58.95500 52.11800 53.58600 scale (grids/A): 2.717327 object centre (A): -31.92550 1.149000 16.68800 number of atom coordinates read : 3016 total number of charged atoms : 2872 net assigned charge : 1.000014 assigned positive charge : 449.5391 centred at (gu) : 97.62893 89.85627 90.36220 assigned negative charge : -448.5404 centred at (gu) : 97.89380 89.78722 90.32957 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 186659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24162 grid for indexing accessible points = 1.400000 m= 93134 mr = 139873 m= 30471 mr = 76568 m= 6201 mr = 24241 m= 668 mr = 4624 m= 27 mr = 417 m= 0 mr = 11 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 9021 time to turn everything in is 1.090000 number of dielectric boundary points 71426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 22973 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) : 1.811551 object centre at (A) : -31.92550 1.149000 16.68800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3550680E-02 -0.2411837 midg,1,midg; midg,igrid,midg -9.8290425E-03 0.1410464 1,midg,midg; igrid,midg,midg 0.3364554 0.1382679 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 1.420000 now iterating at: 11:26:17 rms-change max change #iterations 9.927748 386.1688 at 10iterations 5.758820 119.8321 at 20iterations 3.319662 73.15122 at 30iterations 1.904609 38.35233 at 40iterations 1.095024 22.00341 at 50iterations 0.6256225 12.82646 at 60iterations 0.3586069 6.928469 at 70iterations 0.2047927 4.026838 at 80iterations 0.1169560 2.102278 at 90iterations 6.6841476E-02 1.505314 at 100iterations 3.8205832E-02 0.6978798 at 110iterations 2.1779299E-02 0.4024048 at 120iterations 1.2449544E-02 0.2256165 at 130iterations 7.1160463E-03 0.1313734 at 140iterations 4.0808632E-03 7.8025818E-02 at 150iterations 2.3519818E-03 4.6279907E-02 at 160iterations 1.3640615E-03 2.5371552E-02 at 170iterations 7.9904427E-04 1.4640808E-02 at 180iterations finished qdiffx linear iterations at : 11:26:34 total time elapsed so far: 16.58000 # loops : 180 mean,max change (kT/e) : 7.9904427E-04 1.4640808E-02 energy calculations done at 16.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.71000 DelPhi exited at 11:26:35 16.708u 0.346s 0:19.84 85.8% 0+0k 0+0io 0pf+0w