Wed Dec 28 11:01:51 PST 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 Wed Dec 28 2011 at 11:01:51 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 0.6226497 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): -35.24000 10.57100 ymin,ymax (A): 0.3200001 41.47600 zmin,zma (A): -0.6670000 56.50800 x,y,z range (A): 45.81100 41.15600 57.17500 scale (grids/A): 0.6226497 object centre (A): -12.33450 20.89800 27.92050 number of atom coordinates read : 1970 total number of charged atoms : 1770 net assigned charge : -21.95202 assigned positive charge : 267.1224 centred at (gu) : 90.25420 89.78199 90.00655 assigned negative charge : -289.0742 centred at (gu) : 90.15138 89.96224 89.99120 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5212 nv = 96 ne = 84 npr = 40222 no. pairs analyzed = 40222 no. exposed pairs = 2473 no. arc points = 17128 no. surface atoms = 843 nbur = 1127 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 264 mr = 2863 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1675 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9985466E-08 -1.8396522E-08 midg,1,midg; midg,igrid,midg -1.0176287E-08 -2.7696649E-08 1,midg,midg; igrid,midg,midg -2.3442064E-08 -1.4499120E-08 gauss-seidel spectral radius is 0.9865875 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 11:01:52 rms-change max change #iterations 0.1180219 22.02995 at 10iterations 1.0930038E-02 1.804932 at 20iterations 1.0043792E-03 0.1605377 at 30iterations 9.2980423E-05 1.2519836E-02 at 40iterations 8.6395439E-06 1.4038086E-03 at 50iterations finished qdiffx linear iterations at : 11:01:56 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 8.6395439E-06 1.4038086E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 11:01:58 4.676u 0.511s 0:06.39 81.0% 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 Wed Dec 28 2011 at 11:01:58 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 1.867949 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): -35.24000 10.57100 ymin,ymax (A): 0.3200001 41.47600 zmin,zma (A): -0.6670000 56.50800 x,y,z range (A): 45.81100 41.15600 57.17500 scale (grids/A): 1.867949 object centre (A): -12.33450 20.89800 27.92050 number of atom coordinates read : 1970 total number of charged atoms : 1770 net assigned charge : -21.95202 assigned positive charge : 267.1224 centred at (gu) : 90.76279 89.34624 90.01974 assigned negative charge : -289.0742 centred at (gu) : 90.45444 89.88693 89.97383 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 56245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17128 grid for indexing accessible points = 1.400000 m= 20811 mr = 38806 m= 3144 mr = 15761 m= 183 mr = 1992 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 171 time to turn everything in is 0.5500000 number of dielectric boundary points 23754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 13931 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) : 0.6226497 object centre at (A) : -12.33450 20.89800 27.92050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4194223E-02 -5.5398516E-02 midg,1,midg; midg,igrid,midg -1.6250359E-02 -4.1757938E-02 1,midg,midg; igrid,midg,midg -2.6885886E-02 -3.1201556E-02 gauss-seidel spectral radius is 0.9985073 estimated iterations to convergence 205 setup time was (sec) 0.9300000 now iterating at: 11:01:59 rms-change max change #iterations 3.441006 161.9030 at 10iterations 1.562238 55.24399 at 20iterations 0.7033175 23.90882 at 30iterations 0.3183505 11.38860 at 40iterations 0.1438829 5.836826 at 50iterations 6.5248214E-02 2.410759 at 60iterations 2.9399564E-02 1.052265 at 70iterations 1.3295815E-02 0.5372238 at 80iterations 6.0266964E-03 0.2149048 at 90iterations 2.7250845E-03 9.2384338E-02 at 100iterations 1.2349640E-03 4.4147491E-02 at 110iterations 5.5762066E-04 2.0210266E-02 at 120iterations finished qdiffx linear iterations at : 11:02:10 total time elapsed so far: 11.50000 # loops : 120 mean,max change (kT/e) : 5.5762066E-04 2.0210266E-02 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 11:02:11 11.700u 0.515s 0:12.90 94.6% 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 Wed Dec 28 2011 at 11:02:11 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 2.801924 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): -35.24000 10.57100 ymin,ymax (A): 0.3200001 41.47600 zmin,zma (A): -0.6670000 56.50800 x,y,z range (A): 45.81100 41.15600 57.17500 scale (grids/A): 2.801924 object centre (A): -12.33450 20.89800 27.92050 number of atom coordinates read : 1970 total number of charged atoms : 1770 net assigned charge : -21.95202 assigned positive charge : 267.1224 centred at (gu) : 91.14423 89.01955 90.02975 assigned negative charge : -289.0742 centred at (gu) : 90.68160 89.83047 89.96078 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 129745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17128 grid for indexing accessible points = 1.400000 m= 66987 mr = 93715 m= 24611 mr = 55378 m= 5644 mr = 20236 m= 739 mr = 4369 m= 58 mr = 516 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 624 time to turn everything in is 1.370000 number of dielectric boundary points 53546 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 14160 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) : 1.867949 object centre at (A) : -12.33450 20.89800 27.92050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8027416 -0.8342361 midg,1,midg; midg,igrid,midg -0.1821031 -0.4490640 1,midg,midg; igrid,midg,midg -0.2798001 -0.3344955 gauss-seidel spectral radius is 0.9992056 estimated iterations to convergence 280 setup time was (sec) 1.790000 now iterating at: 11:02:13 rms-change max change #iterations 8.125118 326.9710 at 10iterations 4.646935 152.7205 at 20iterations 2.621844 63.00183 at 30iterations 1.480745 33.14557 at 40iterations 0.8345346 18.65218 at 50iterations 0.4701984 10.21347 at 60iterations 0.2646997 5.758419 at 70iterations 0.1489448 3.424072 at 80iterations 8.3665088E-02 1.763023 at 90iterations 4.7066417E-02 0.9826536 at 100iterations 2.6463775E-02 0.5518637 at 110iterations 1.4883874E-02 0.3371582 at 120iterations 8.3723599E-03 0.1699215 at 130iterations 4.6956050E-03 0.1020927 at 140iterations 2.6447352E-03 5.5886269E-02 at 150iterations 1.4874254E-03 3.1204224E-02 at 160iterations 8.3486817E-04 1.7471313E-02 at 170iterations 4.6801326E-04 1.0568619E-02 at 180iterations finished qdiffx linear iterations at : 11:02:30 total time elapsed so far: 18.61000 # loops : 180 mean,max change (kT/e) : 4.6801326E-04 1.0568619E-02 energy calculations done at 18.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.81000 DelPhi exited at 11:02:32 18.815u 0.473s 0:20.94 92.0% 0+0k 0+0io 0pf+0w