Sun Oct 9 10:35:32 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+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 Sun Oct 9 2011 at 10:35:32 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2944 !!! WARNING: CME 114 has a net charge of -0.3480 !!! WARNING: CME 220 has a net charge of -0.3480 !!! WARNING: CME 316 has a net charge of -0.3480 !!! WARNING: CME 457 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 0.5828231 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): -50.19000 10.89200 ymin,ymax (A): -26.42500 23.82400 zmin,zma (A): -29.86200 26.47400 x,y,z range (A): 61.08200 50.24900 56.33600 scale (grids/A): 0.5828231 object centre (A): -19.64900 -1.300500 -1.694000 number of atom coordinates read : 2944 total number of charged atoms : 2841 net assigned charge : -1.166966 assigned positive charge : 435.9079 centred at (gu) : 89.50930 91.44996 91.60635 assigned negative charge : -437.0768 centred at (gu) : 89.49657 91.43977 91.58060 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7009 nv = 96 ne = 84 npr = 57146 no. pairs analyzed = 57146 no. exposed pairs = 4036 no. arc points = 28726 no. surface atoms = 1326 nbur = 1618 mkacc time = 8.9999996E-02 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= 371 mr = 3620 m= 1 mr = 21 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 0.2300000 number of dielectric boundary points 3740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2841 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8700 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2283895E-10 4.6820042E-10 midg,1,midg; midg,igrid,midg -3.8327577E-10 -6.7718699E-11 1,midg,midg; igrid,midg,midg -6.6621025E-10 4.8398768E-12 gauss-seidel spectral radius is 0.9848161 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 10:35:33 rms-change max change #iterations 9.8575138E-02 15.45222 at 10iterations 8.1409812E-03 1.315580 at 20iterations 7.4599701E-04 0.1136227 at 30iterations 1.0810831E-04 1.7513275E-02 at 40iterations 2.5137308E-05 4.1351318E-03 at 50iterations finished qdiffx linear iterations at : 10:35:36 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.5137308E-05 4.1351318E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 10:35:36 3.456u 0.168s 0:04.07 88.6% 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 Sun Oct 9 2011 at 10:35:37 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2944 !!! WARNING: CME 114 has a net charge of -0.3480 !!! WARNING: CME 220 has a net charge of -0.3480 !!! WARNING: CME 316 has a net charge of -0.3480 !!! WARNING: CME 457 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 1.748469 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): -50.19000 10.89200 ymin,ymax (A): -26.42500 23.82400 zmin,zma (A): -29.86200 26.47400 x,y,z range (A): 61.08200 50.24900 56.33600 scale (grids/A): 1.748469 object centre (A): -19.64900 -1.300500 -1.694000 number of atom coordinates read : 2944 total number of charged atoms : 2841 net assigned charge : -1.166966 assigned positive charge : 435.9079 centred at (gu) : 88.52683 94.34918 94.81844 assigned negative charge : -437.0768 centred at (gu) : 88.48946 94.31938 94.74181 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75831 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28726 grid for indexing accessible points = 1.400000 m= 25965 mr = 50935 m= 3693 mr = 18000 m= 177 mr = 2026 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 34691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 22149 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) : 0.5828231 object centre at (A) : -19.64900 -1.300500 -1.694000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0331741E-03 5.1478893E-03 midg,1,midg; midg,igrid,midg 4.0614754E-03 9.3106218E-03 1,midg,midg; igrid,midg,midg 9.1796322E-03 -1.1601455E-02 gauss-seidel spectral radius is 0.9984449 estimated iterations to convergence 201 setup time was (sec) 0.5900000 now iterating at: 10:35:37 rms-change max change #iterations 3.832203 175.5677 at 10iterations 1.691110 69.03036 at 20iterations 0.7513195 30.49704 at 30iterations 0.3345776 13.20646 at 40iterations 0.1492173 5.377851 at 50iterations 6.6348270E-02 2.213276 at 60iterations 2.9536599E-02 0.9489335 at 70iterations 1.3208523E-02 0.4470223 at 80iterations 5.8849407E-03 0.1945333 at 90iterations 2.6316494E-03 8.4156036E-02 at 100iterations 1.1797600E-03 3.8198471E-02 at 110iterations 5.3392077E-04 1.7079353E-02 at 120iterations finished qdiffx linear iterations at : 10:35:44 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 5.3392077E-04 1.7079353E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 10:35:45 7.721u 0.184s 0:08.32 94.9% 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 10:35:45 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2944 !!! WARNING: CME 114 has a net charge of -0.3480 !!! WARNING: CME 220 has a net charge of -0.3480 !!! WARNING: CME 316 has a net charge of -0.3480 !!! WARNING: CME 457 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 2.622704 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): -50.19000 10.89200 ymin,ymax (A): -26.42500 23.82400 zmin,zma (A): -29.86200 26.47400 x,y,z range (A): 61.08200 50.24900 56.33600 scale (grids/A): 2.622704 object centre (A): -19.64900 -1.300500 -1.694000 number of atom coordinates read : 2944 total number of charged atoms : 2841 net assigned charge : -1.166966 assigned positive charge : 435.9079 centred at (gu) : 87.79014 96.52351 97.22746 assigned negative charge : -437.0768 centred at (gu) : 87.73425 96.47915 97.11266 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 175866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28726 grid for indexing accessible points = 1.400000 m= 84561 mr = 124908 m= 28880 mr = 66471 m= 6300 mr = 22062 m= 657 mr = 4240 m= 25 mr = 332 m= 0 mr = 9 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 78267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 22717 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) : 1.748469 object centre at (A) : -19.64900 -1.300500 -1.694000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1187548 7.7746965E-02 midg,1,midg; midg,igrid,midg 0.1159820 0.1280122 1,midg,midg; igrid,midg,midg 0.2077140 -0.1650586 gauss-seidel spectral radius is 0.9992216 estimated iterations to convergence 283 setup time was (sec) 1.160000 now iterating at: 10:35:46 rms-change max change #iterations 9.566431 267.4814 at 10iterations 5.603251 196.3505 at 20iterations 3.248274 84.34306 at 30iterations 1.873509 39.71246 at 40iterations 1.077668 25.14406 at 50iterations 0.6165146 15.24953 at 60iterations 0.3525970 7.039389 at 70iterations 0.2013054 4.103058 at 80iterations 0.1146224 2.261561 at 90iterations 6.5216154E-02 1.247799 at 100iterations 3.7097890E-02 0.6848305 at 110iterations 2.1085983E-02 0.4119072 at 120iterations 1.1964575E-02 0.2338238 at 130iterations 6.7879045E-03 0.1231914 at 140iterations 3.8548349E-03 7.2059155E-02 at 150iterations 2.1840094E-03 4.2961121E-02 at 160iterations 1.2430549E-03 2.2296906E-02 at 170iterations 7.0755160E-04 1.3595581E-02 at 180iterations finished qdiffx linear iterations at : 10:35:58 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 7.0755160E-04 1.3595581E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 10:35:58 12.547u 0.213s 0:13.09 97.4% 0+0k 0+0io 0pf+0w