Sat Oct 8 13:46:15 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 Sat Oct 8 2011 at 13:46:15 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6397240 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): -11.97200 42.38000 ymin,ymax (A): -22.68000 22.98100 zmin,zma (A): -7.718000 47.93100 x,y,z range (A): 54.35200 45.66100 55.64900 scale (grids/A): 0.6397240 object centre (A): 15.20400 0.1504993 20.10650 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 1.4008060E-02 assigned positive charge : 456.0876 centred at (gu) : 89.13774 89.53959 91.61376 assigned negative charge : -456.0743 centred at (gu) : 89.13108 89.45207 91.52102 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8170 nv = 96 ne = 84 npr = 63443 no. pairs analyzed = 63443 no. exposed pairs = 3478 no. arc points = 24091 no. surface atoms = 1186 nbur = 1845 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 4749 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2394 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10052 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0484686E-09 1.7588365E-08 midg,1,midg; midg,igrid,midg -1.3392509E-08 1.0519339E-08 1,midg,midg; igrid,midg,midg -1.2448224E-09 6.4375522E-10 gauss-seidel spectral radius is 0.9873717 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 13:46:16 rms-change max change #iterations 0.1601470 23.97442 at 10iterations 1.6633555E-02 2.279583 at 20iterations 1.6979115E-03 0.2598343 at 30iterations 1.9002217E-04 2.7252197E-02 at 40iterations 2.6047761E-05 3.2920837E-03 at 50iterations finished qdiffx linear iterations at : 13:46:20 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 2.6047761E-05 3.2920837E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 13:46:20 4.177u 0.273s 0:04.74 93.6% 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 8 2011 at 13:46:20 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.919172 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): -11.97200 42.38000 ymin,ymax (A): -22.68000 22.98100 zmin,zma (A): -7.718000 47.93100 x,y,z range (A): 54.35200 45.66100 55.64900 scale (grids/A): 1.919172 object centre (A): 15.20400 0.1504993 20.10650 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 1.4008060E-02 assigned positive charge : 456.0876 centred at (gu) : 87.41245 88.61824 94.84093 assigned negative charge : -456.0743 centred at (gu) : 87.39311 88.35581 94.56284 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 89653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24091 grid for indexing accessible points = 1.400000 m= 32577 mr = 64857 m= 4924 mr = 24488 m= 322 mr = 3054 m= 4 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 211 time to turn everything in is 0.7900000 number of dielectric boundary points 34961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 22733 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) : 0.6397240 object centre at (A) : 15.20400 0.1504993 20.10650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9745456E-02 2.2175401E-02 midg,1,midg; midg,igrid,midg -2.3907607E-03 2.4395216E-02 1,midg,midg; igrid,midg,midg -3.0086637E-02 7.6090312E-03 gauss-seidel spectral radius is 0.9986903 estimated iterations to convergence 219 setup time was (sec) 1.090000 now iterating at: 13:46:21 rms-change max change #iterations 4.743556 186.2908 at 10iterations 2.267423 79.56465 at 20iterations 1.076820 30.89503 at 30iterations 0.5136056 14.98255 at 40iterations 0.2450979 7.168419 at 50iterations 0.1167938 3.291485 at 60iterations 5.5510908E-02 1.568004 at 70iterations 2.6541209E-02 0.7526684 at 80iterations 1.2632852E-02 0.3696556 at 90iterations 6.0530188E-03 0.1606293 at 100iterations 2.8785956E-03 8.1962585E-02 at 110iterations 1.3798068E-03 4.0317535E-02 at 120iterations finished qdiffx linear iterations at : 13:46:30 total time elapsed so far: 9.570000 # loops : 120 mean,max change (kT/e) : 1.3798068E-03 4.0317535E-02 energy calculations done at 9.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.750000 DelPhi exited at 13:46:30 9.752u 0.295s 0:10.34 97.0% 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 Sat Oct 8 2011 at 13:46:31 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.878758 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): -11.97200 42.38000 ymin,ymax (A): -22.68000 22.98100 zmin,zma (A): -7.718000 47.93100 x,y,z range (A): 54.35200 45.66100 55.64900 scale (grids/A): 2.878758 object centre (A): 15.20400 0.1504993 20.10650 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 1.4008060E-02 assigned positive charge : 456.0876 centred at (gu) : 86.11845 87.92733 97.26131 assigned negative charge : -456.0743 centred at (gu) : 86.08959 87.53354 96.84421 start vw surface at 0.1700000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 207738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24091 grid for indexing accessible points = 1.400000 m= 106947 mr = 156508 m= 37364 mr = 89072 m= 8654 mr = 30382 m= 1304 mr = 6412 m= 83 mr = 888 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 753 time to turn everything in is 2.020000 number of dielectric boundary points 78797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 23072 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) : 1.919172 object centre at (A) : 15.20400 0.1504993 20.10650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1875533E-02 0.3070719 midg,1,midg; midg,igrid,midg -2.2489477E-02 0.3184403 1,midg,midg; igrid,midg,midg -0.4817137 0.1429805 gauss-seidel spectral radius is 0.9992756 estimated iterations to convergence 293 setup time was (sec) 2.360000 now iterating at: 13:46:33 rms-change max change #iterations 10.96895 427.6049 at 10iterations 6.438804 131.5334 at 20iterations 3.749245 78.88142 at 30iterations 2.188578 39.10802 at 40iterations 1.268640 22.54587 at 50iterations 0.7369298 12.46212 at 60iterations 0.4280593 7.697750 at 70iterations 0.2485638 4.614365 at 80iterations 0.1438419 2.375000 at 90iterations 8.3253436E-02 1.383038 at 100iterations 4.8207149E-02 0.7356834 at 110iterations 2.7894689E-02 0.4552765 at 120iterations 1.6163720E-02 0.2480712 at 130iterations 9.3864985E-03 0.1491184 at 140iterations 5.4368242E-03 8.9792728E-02 at 150iterations 3.1656420E-03 5.1699162E-02 at 160iterations 1.8446126E-03 3.1455994E-02 at 170iterations 1.0827639E-03 1.8697739E-02 at 180iterations finished qdiffx linear iterations at : 13:46:47 total time elapsed so far: 16.47000 # loops : 180 mean,max change (kT/e) : 1.0827639E-03 1.8697739E-02 energy calculations done at 16.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.65000 DelPhi exited at 13:46:48 16.655u 0.317s 0:17.31 97.9% 0+0k 0+0io 0pf+0w