Sun Oct 9 07:34:32 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 Sun Oct 9 2011 at 07:34:32 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 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: 0.7654103 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): -14.21700 26.41000 ymin,ymax (A): 3.756000 46.53500 zmin,zma (A): -1.407000 45.10400 x,y,z range (A): 40.62700 42.77900 46.51100 scale (grids/A): 0.7654103 object centre (A): 6.096500 25.14550 21.84850 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 242.4202 centred at (gu) : 89.88235 89.78159 89.73185 assigned negative charge : -251.9201 centred at (gu) : 90.15497 89.97597 90.04868 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6547 nv = 96 ne = 84 npr = 35151 no. pairs analyzed = 35151 no. exposed pairs = 2111 no. arc points = 14944 no. surface atoms = 719 nbur = 930 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 507 mr = 3630 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 102 time to turn everything in is 0.2300000 number of dielectric boundary points 3308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1104 ## 77 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6700 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2725567E-07 -6.8305400E-07 midg,1,midg; midg,igrid,midg -3.4674539E-08 -5.2641440E-07 1,midg,midg; igrid,midg,midg 6.6741705E-08 -6.4162839E-07 gauss-seidel spectral radius is 0.9910530 estimated iterations to convergence 86 setup time was (sec) 0.4800000 now iterating at: 07:34:33 rms-change max change #iterations 0.2498147 34.64423 at 10iterations 3.5366755E-02 4.768434 at 20iterations 5.0873253E-03 0.6691132 at 30iterations 7.3257805E-04 0.1000443 at 40iterations 1.0378988E-04 1.4011383E-02 at 50iterations finished qdiffx linear iterations at : 07:34:36 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.0378988E-04 1.4011383E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 07:34:36 3.398u 0.221s 0:03.90 92.5% 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 Sun Oct 9 2011 at 07:34:36 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.296231 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): -14.21700 26.41000 ymin,ymax (A): 3.756000 46.53500 zmin,zma (A): -1.407000 45.10400 x,y,z range (A): 40.62700 42.77900 46.51100 scale (grids/A): 2.296231 object centre (A): 6.096500 25.14550 21.84850 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 242.4202 centred at (gu) : 89.64725 89.34499 89.19576 assigned negative charge : -251.9201 centred at (gu) : 90.46487 89.92788 90.14599 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14944 grid for indexing accessible points = 1.400000 m= 28358 mr = 46626 m= 6505 mr = 21930 m= 682 mr = 4604 m= 28 mr = 384 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2436 time to turn everything in is 0.5400000 number of dielectric boundary points 30420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 12061 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) : 0.7654103 object centre at (A) : 6.096500 25.14550 21.84850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6849921E-02 -0.1918852 midg,1,midg; midg,igrid,midg -2.9492043E-02 -9.8532371E-02 1,midg,midg; igrid,midg,midg 5.0963260E-02 -6.7605108E-02 gauss-seidel spectral radius is 0.9989429 estimated iterations to convergence 243 setup time was (sec) 0.8600000 now iterating at: 07:34:37 rms-change max change #iterations 4.726426 270.6596 at 10iterations 2.418712 84.07005 at 20iterations 1.231040 41.93759 at 30iterations 0.6326401 19.56283 at 40iterations 0.3234866 9.473082 at 50iterations 0.1663247 5.261051 at 60iterations 8.5139275E-02 2.531054 at 70iterations 4.3635201E-02 1.426938 at 80iterations 2.2358509E-02 0.6805372 at 90iterations 1.1462110E-02 0.3544197 at 100iterations 5.8717798E-03 0.1734333 at 110iterations 3.0066047E-03 9.0698242E-02 at 120iterations finished qdiffx linear iterations at : 07:34:44 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 3.0066047E-03 9.0698242E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 07:34:45 7.842u 0.246s 0:08.38 96.4% 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 Sun Oct 9 2011 at 07:34:45 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 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: 3.444346 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): -14.21700 26.41000 ymin,ymax (A): 3.756000 46.53500 zmin,zma (A): -1.407000 45.10400 x,y,z range (A): 40.62700 42.77900 46.51100 scale (grids/A): 3.444346 object centre (A): 6.096500 25.14550 21.84850 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 242.4202 centred at (gu) : 89.47093 89.01755 88.79375 assigned negative charge : -251.9201 centred at (gu) : 90.69732 89.89188 90.21897 start vw surface at 0.1200000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 157072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14944 grid for indexing accessible points = 1.400000 m= 85019 mr = 112099 m= 38690 mr = 70906 m= 12636 mr = 32535 m= 2783 mr = 10201 m= 362 mr = 2065 m= 20 mr = 235 m= 0 mr = 4 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 8144 time to turn everything in is 1.680000 number of dielectric boundary points 68537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 12096 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) : 2.296231 object centre at (A) : 6.096500 25.14550 21.84850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1772499 -1.787625 midg,1,midg; midg,igrid,midg -0.2881072 -0.7389572 1,midg,midg; igrid,midg,midg 0.5788358 -0.3837592 gauss-seidel spectral radius is 0.9993185 estimated iterations to convergence 302 setup time was (sec) 1.990000 now iterating at: 07:34:47 rms-change max change #iterations 10.00349 278.6106 at 10iterations 5.865234 118.9199 at 20iterations 3.446394 65.92989 at 30iterations 2.027102 34.91787 at 40iterations 1.188134 20.92853 at 50iterations 0.6956285 12.97238 at 60iterations 0.4079003 7.678577 at 70iterations 0.2399679 4.400694 at 80iterations 0.1408086 2.647100 at 90iterations 8.2410835E-02 1.402805 at 100iterations 4.8389573E-02 0.8075829 at 110iterations 2.8399669E-02 0.5187125 at 120iterations 1.6666066E-02 0.2820539 at 130iterations 9.7588841E-03 0.1772938 at 140iterations 5.7382355E-03 9.0782166E-02 at 150iterations 3.3687495E-03 5.8731079E-02 at 160iterations 1.9757680E-03 3.4695625E-02 at 170iterations 1.1633779E-03 2.0179331E-02 at 180iterations finished qdiffx linear iterations at : 07:34:58 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 1.1633779E-03 2.0179331E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 07:34:59 13.206u 0.294s 0:13.78 97.8% 0+0k 0+0io 0pf+0w