Tue Oct 11 06:36:52 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 Tue Oct 11 2011 at 06:36:52 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7047412 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): -20.02900 23.91300 ymin,ymax (A): -28.45900 12.30500 zmin,zma (A): -13.89000 36.62500 x,y,z range (A): 43.94200 40.76400 50.51500 scale (grids/A): 0.7047412 object centre (A): 1.942000 -8.077000 11.36750 number of atom coordinates read : 2073 total number of charged atoms : 1939 net assigned charge : 6.931010 assigned positive charge : 314.7471 centred at (gu) : 90.09103 90.28633 89.42887 assigned negative charge : -307.8161 centred at (gu) : 89.90291 90.26283 89.40965 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6955 nv = 96 ne = 84 npr = 41824 no. pairs analyzed = 41824 no. exposed pairs = 2485 no. arc points = 16892 no. surface atoms = 843 nbur = 1230 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4031 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1625 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7790 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1214670E-08 5.7147869E-08 midg,1,midg; midg,igrid,midg 4.1778915E-08 6.9325992E-08 1,midg,midg; igrid,midg,midg -3.2522795E-08 1.4218092E-07 gauss-seidel spectral radius is 0.9895025 estimated iterations to convergence 79 setup time was (sec) 0.4800000 now iterating at: 06:36:53 rms-change max change #iterations 0.2007674 30.43214 at 10iterations 2.4984382E-02 3.585693 at 20iterations 3.3905196E-03 0.4698982 at 30iterations 5.7699840E-04 7.4218750E-02 at 40iterations 1.4349411E-04 1.8936157E-02 at 50iterations finished qdiffx linear iterations at : 06:36:55 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.4349411E-04 1.8936157E-02 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 06:36:56 3.141u 0.170s 0:03.87 85.5% 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 Tue Oct 11 2011 at 06:36:56 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.114223 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): -20.02900 23.91300 ymin,ymax (A): -28.45900 12.30500 zmin,zma (A): -13.89000 36.62500 x,y,z range (A): 43.94200 40.76400 50.51500 scale (grids/A): 2.114223 object centre (A): 1.942000 -8.077000 11.36750 number of atom coordinates read : 2073 total number of charged atoms : 1939 net assigned charge : 6.931010 assigned positive charge : 314.7471 centred at (gu) : 90.27296 90.85873 88.28627 assigned negative charge : -307.8161 centred at (gu) : 89.70877 90.78855 88.22913 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 74191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16892 grid for indexing accessible points = 1.400000 m= 29409 mr = 53111 m= 5725 mr = 22334 m= 505 mr = 3811 m= 14 mr = 260 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 30327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 15403 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) : 0.7047412 object centre at (A) : 1.942000 -8.077000 11.36750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7301475E-02 3.9835677E-02 midg,1,midg; midg,igrid,midg 7.1519539E-03 3.1018913E-02 1,midg,midg; igrid,midg,midg 4.5772884E-03 4.0705435E-02 gauss-seidel spectral radius is 0.9988213 estimated iterations to convergence 231 setup time was (sec) 0.7800000 now iterating at: 06:36:57 rms-change max change #iterations 4.576522 174.7921 at 10iterations 2.256125 79.12978 at 20iterations 1.117492 34.78587 at 30iterations 0.5546396 17.63992 at 40iterations 0.2751302 7.686466 at 50iterations 0.1358784 4.241708 at 60iterations 6.7270204E-02 2.042145 at 70iterations 3.3527471E-02 1.012826 at 80iterations 1.6633315E-02 0.4775107 at 90iterations 8.3206948E-03 0.2633038 at 100iterations 4.1738804E-03 0.1253891 at 110iterations 2.1124308E-03 6.5719604E-02 at 120iterations finished qdiffx linear iterations at : 06:37:03 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 2.1124308E-03 6.5719604E-02 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 06:37:04 7.072u 0.222s 0:07.79 93.5% 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 Tue Oct 11 2011 at 06:37:04 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.171335 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): -20.02900 23.91300 ymin,ymax (A): -28.45900 12.30500 zmin,zma (A): -13.89000 36.62500 x,y,z range (A): 43.94200 40.76400 50.51500 scale (grids/A): 3.171335 object centre (A): 1.942000 -8.077000 11.36750 number of atom coordinates read : 2073 total number of charged atoms : 1939 net assigned charge : 6.931010 assigned positive charge : 314.7471 centred at (gu) : 90.40958 91.28822 87.42940 assigned negative charge : -307.8161 centred at (gu) : 89.56326 91.18284 87.34370 start vw surface at 0.1200000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 171163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16892 grid for indexing accessible points = 1.400000 m= 92550 mr = 127803 m= 37042 mr = 77073 m= 10663 mr = 30461 m= 2085 mr = 8254 m= 229 mr = 1520 m= 7 mr = 155 m= 0 mr = 2 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.680000 number of dielectric boundary points 68471 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 15512 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) : 2.114223 object centre at (A) : 1.942000 -8.077000 11.36750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6129262 0.3364790 midg,1,midg; midg,igrid,midg 3.4742031E-02 0.2372744 1,midg,midg; igrid,midg,midg 0.1399516 0.3273951 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 1.970000 now iterating at: 06:37:06 rms-change max change #iterations 10.16481 346.8716 at 10iterations 5.996066 126.5436 at 20iterations 3.526495 76.05269 at 30iterations 2.076190 39.40255 at 40iterations 1.216177 26.27835 at 50iterations 0.7139547 15.35302 at 60iterations 0.4178877 7.629835 at 70iterations 0.2443169 4.327431 at 80iterations 0.1432905 2.796425 at 90iterations 8.3875224E-02 1.703812 at 100iterations 4.9172673E-02 1.005944 at 110iterations 2.9033799E-02 0.5022583 at 120iterations 1.7239034E-02 0.3555088 at 130iterations 1.0407455E-02 0.2152023 at 140iterations 6.4768270E-03 0.1237869 at 150iterations 4.1694152E-03 8.6154938E-02 at 160iterations 2.8510420E-03 5.4794312E-02 at 170iterations 2.0494501E-03 3.7538528E-02 at 180iterations finished qdiffx linear iterations at : 06:37:16 total time elapsed so far: 11.51000 # loops : 180 mean,max change (kT/e) : 2.0494501E-03 3.7538528E-02 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 06:37:16 11.688u 0.207s 0:12.52 94.8% 0+0k 0+0io 0pf+0w