Mon Oct 10 17:04:58 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 17:04:58 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6218123 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): -8.336000 45.11600 ymin,ymax (A): -6.639000 44.34800 zmin,zma (A): 30.97800 88.23000 x,y,z range (A): 53.45200 50.98700 57.25200 scale (grids/A): 0.6218123 object centre (A): 18.39000 18.85450 59.60400 number of atom coordinates read : 2588 total number of charged atoms : 2454 net assigned charge : 12.50002 assigned positive charge : 380.3867 centred at (gu) : 90.23820 90.92025 90.44917 assigned negative charge : -367.8875 centred at (gu) : 90.08109 90.83061 90.46294 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6846 nv = 96 ne = 84 npr = 52369 no. pairs analyzed = 52369 no. exposed pairs = 3225 no. arc points = 22922 no. surface atoms = 1105 nbur = 1483 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3696 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2360 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8317 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0422275E-08 1.0598312E-08 midg,1,midg; midg,igrid,midg 3.7951984E-09 2.0089349E-08 1,midg,midg; igrid,midg,midg -3.0135880E-11 2.1911653E-08 gauss-seidel spectral radius is 0.9866112 estimated iterations to convergence 71 setup time was (sec) 0.3800000 now iterating at: 17:04:58 rms-change max change #iterations 0.1286492 19.39312 at 10iterations 1.1736200E-02 1.607123 at 20iterations 1.0953564E-03 0.1981430 at 30iterations 1.0138443E-04 1.6263962E-02 at 40iterations 9.4822208E-06 1.3566017E-03 at 50iterations finished qdiffx linear iterations at : 17:05:01 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 9.4822208E-06 1.3566017E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 17:05:02 3.342u 0.173s 0:04.26 82.3% 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 17:05:02 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.865437 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): -8.336000 45.11600 ymin,ymax (A): -6.639000 44.34800 zmin,zma (A): 30.97800 88.23000 x,y,z range (A): 53.45200 50.98700 57.25200 scale (grids/A): 1.865437 object centre (A): 18.39000 18.85450 59.60400 number of atom coordinates read : 2588 total number of charged atoms : 2454 net assigned charge : 12.50002 assigned positive charge : 380.3867 centred at (gu) : 90.71409 92.76010 91.34675 assigned negative charge : -367.8875 centred at (gu) : 90.24295 92.49158 91.38868 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 73910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22922 grid for indexing accessible points = 1.400000 m= 26413 mr = 50818 m= 4076 mr = 19313 m= 204 mr = 2402 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 120 time to turn everything in is 0.3500000 number of dielectric boundary points 32023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19256 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) : 0.6218123 object centre at (A) : 18.39000 18.85450 59.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8411727E-03 6.4130216E-03 midg,1,midg; midg,igrid,midg 1.7045312E-02 5.8623746E-02 1,midg,midg; igrid,midg,midg -1.2291241E-02 3.1429503E-02 gauss-seidel spectral radius is 0.9985827 estimated iterations to convergence 211 setup time was (sec) 0.5600000 now iterating at: 17:05:03 rms-change max change #iterations 3.963036 162.9236 at 10iterations 1.837035 62.58284 at 20iterations 0.8457667 27.23366 at 30iterations 0.3896260 12.07931 at 40iterations 0.1799566 5.831017 at 50iterations 8.2790256E-02 2.602592 at 60iterations 3.8294677E-02 1.193285 at 70iterations 1.7714292E-02 0.5259333 at 80iterations 8.1589222E-03 0.2636986 at 90iterations 3.7783694E-03 0.1155701 at 100iterations 1.7422916E-03 5.0813198E-02 at 110iterations 8.0649229E-04 2.5344849E-02 at 120iterations finished qdiffx linear iterations at : 17:05:10 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 8.0649229E-04 2.5344849E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 17:05:11 7.689u 0.202s 0:09.33 84.4% 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 17:05:12 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.798156 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): -8.336000 45.11600 ymin,ymax (A): -6.639000 44.34800 zmin,zma (A): 30.97800 88.23000 x,y,z range (A): 53.45200 50.98700 57.25200 scale (grids/A): 2.798156 object centre (A): 18.39000 18.85450 59.60400 number of atom coordinates read : 2588 total number of charged atoms : 2454 net assigned charge : 12.50002 assigned positive charge : 380.3867 centred at (gu) : 91.07095 94.14009 92.02000 assigned negative charge : -367.8875 centred at (gu) : 90.36431 93.73726 92.08286 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 171349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22922 grid for indexing accessible points = 1.400000 m= 85504 mr = 123792 m= 30485 mr = 69588 m= 7216 mr = 24152 m= 980 mr = 5263 m= 62 mr = 545 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 455 time to turn everything in is 0.9300000 number of dielectric boundary points 72236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19631 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) : 1.865437 object centre at (A) : 18.39000 18.85450 59.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0350714E-02 0.1335765 midg,1,midg; midg,igrid,midg 5.6017686E-02 0.6447756 1,midg,midg; igrid,midg,midg -5.2080210E-02 0.2928832 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 1.180000 now iterating at: 17:05:13 rms-change max change #iterations 9.486967 428.6761 at 10iterations 5.566941 135.2738 at 20iterations 3.231306 73.25962 at 30iterations 1.866275 37.91127 at 40iterations 1.075750 21.66449 at 50iterations 0.6197661 11.80020 at 60iterations 0.3562403 7.484742 at 70iterations 0.2047180 3.742065 at 80iterations 0.1170295 2.331767 at 90iterations 6.7200184E-02 1.375958 at 100iterations 3.8468618E-02 0.7435598 at 110iterations 2.1983726E-02 0.3877281 at 120iterations 1.2583480E-02 0.2478628 at 130iterations 7.2218780E-03 0.1382904 at 140iterations 4.1435207E-03 7.4777499E-02 at 150iterations 2.3800139E-03 4.1987300E-02 at 160iterations 1.3612973E-03 2.9808044E-02 at 170iterations 7.8688050E-04 1.6509771E-02 at 180iterations finished qdiffx linear iterations at : 17:05:24 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 7.8688050E-04 1.6509771E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 17:05:25 12.501u 0.196s 0:13.06 97.1% 0+0k 0+0io 0pf+0w