Sun Oct 9 15:56:44 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 15:56:44 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5331 !!! WARNING: HIR 669 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4994669 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): -103.7540 -32.47800 ymin,ymax (A): -56.55900 9.970000 zmin,zma (A): -30.49500 37.05100 x,y,z range (A): 71.27600 66.52900 67.54601 scale (grids/A): 0.4994669 object centre (A): -68.11600 -23.29450 3.278001 number of atom coordinates read : 5331 total number of charged atoms : 5159 net assigned charge : -1.485958 assigned positive charge : 815.7946 centred at (gu) : 89.05943 89.19131 89.13520 assigned negative charge : -817.2874 centred at (gu) : 89.03497 89.26812 89.07197 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8219 nv = 96 ne = 84 npr = 108541 no. pairs analyzed = 108541 no. exposed pairs = 6252 no. arc points = 43333 no. surface atoms = 2090 nbur = 3241 mkacc time = 0.2600000 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 = 1.708000 m= 275 mr = 4417 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.5400000 number of dielectric boundary points 4067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4100 ## 625 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6269465E-10 8.0423786E-11 midg,1,midg; midg,igrid,midg 1.5757362E-10 -1.2339953E-10 1,midg,midg; igrid,midg,midg -7.3616752E-11 2.4760192E-11 gauss-seidel spectral radius is 0.9795340 estimated iterations to convergence 58 setup time was (sec) 0.7700000 now iterating at: 15:56:45 rms-change max change #iterations 6.2864050E-02 9.908686 at 10iterations 5.7949005E-03 1.118406 at 20iterations 1.8664739E-03 0.3677711 at 30iterations 7.2212867E-04 0.1423187 at 40iterations 2.7865809E-04 5.5099487E-02 at 50iterations finished qdiffx linear iterations at : 15:56:47 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.7865809E-04 5.5099487E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:56:48 3.616u 0.156s 0:04.05 92.8% 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 15:56:48 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5331 !!! WARNING: HIR 669 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.498401 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): -103.7540 -32.47800 ymin,ymax (A): -56.55900 9.970000 zmin,zma (A): -30.49500 37.05100 x,y,z range (A): 71.27600 66.52900 67.54601 scale (grids/A): 1.498401 object centre (A): -68.11600 -23.29450 3.278001 number of atom coordinates read : 5331 total number of charged atoms : 5159 net assigned charge : -1.485958 assigned positive charge : 815.7946 centred at (gu) : 87.17696 87.57271 87.40381 assigned negative charge : -817.2874 centred at (gu) : 87.10428 87.80437 87.21593 start vw surface at 0.2400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 94301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43333 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27065 mr = 66553 m= 2270 mr = 18372 m= 42 mr = 905 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3032 time to turn everything in is 0.7000000 number of dielectric boundary points 37848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 547 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 38362 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) : 0.4994669 object centre at (A) : -68.11600 -23.29450 3.278001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3056424E-03 5.0667385E-03 midg,1,midg; midg,igrid,midg 1.4354451E-02 -9.1785202E-03 1,midg,midg; igrid,midg,midg -3.2242108E-02 4.6076947E-03 gauss-seidel spectral radius is 0.9980553 estimated iterations to convergence 180 setup time was (sec) 0.9800000 now iterating at: 15:56:49 rms-change max change #iterations 3.882550 152.5755 at 10iterations 1.574372 51.63979 at 20iterations 0.6395597 20.42394 at 30iterations 0.2594510 8.999777 at 40iterations 0.1053534 3.281605 at 50iterations 4.3009579E-02 1.400864 at 60iterations 1.7983235E-02 0.6363716 at 70iterations 7.8540472E-03 0.3295212 at 80iterations 3.7706592E-03 0.1395912 at 90iterations 2.1196888E-03 9.3078613E-02 at 100iterations 1.3415333E-03 5.4630280E-02 at 110iterations 9.1438403E-04 3.8272858E-02 at 120iterations finished qdiffx linear iterations at : 15:56:56 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 9.1438403E-04 3.8272858E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 15:56:56 7.999u 0.180s 0:08.48 96.3% 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 Sun Oct 9 2011 at 15:56:56 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5331 !!! WARNING: HIR 669 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.247601 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): -103.7540 -32.47800 ymin,ymax (A): -56.55900 9.970000 zmin,zma (A): -30.49500 37.05100 x,y,z range (A): 71.27600 66.52900 67.54601 scale (grids/A): 2.247601 object centre (A): -68.11600 -23.29450 3.278001 number of atom coordinates read : 5331 total number of charged atoms : 5159 net assigned charge : -1.485958 assigned positive charge : 815.7946 centred at (gu) : 85.76503 86.35876 86.10548 assigned negative charge : -817.2874 centred at (gu) : 85.65643 86.70658 85.82381 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 220214 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43333 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 97985 mr = 163433 m= 24279 mr = 77412 m= 3252 mr = 17686 m= 154 mr = 1881 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 10438 time to turn everything in is 1.630000 number of dielectric boundary points 85438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 41138 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) : 1.498401 object centre at (A) : -68.11600 -23.29450 3.278001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8433635E-02 9.9214822E-02 midg,1,midg; midg,igrid,midg 0.3619308 -0.1302509 1,midg,midg; igrid,midg,midg -0.7641976 0.1286469 gauss-seidel spectral radius is 0.9991484 estimated iterations to convergence 271 setup time was (sec) 1.950000 now iterating at: 15:56:58 rms-change max change #iterations 10.62609 244.7432 at 10iterations 6.043113 170.7471 at 20iterations 3.400640 91.94400 at 30iterations 1.911712 41.46785 at 40iterations 1.066134 24.37520 at 50iterations 0.5956764 15.84119 at 60iterations 0.3317336 6.598965 at 70iterations 0.1839218 3.774681 at 80iterations 0.1022847 1.804474 at 90iterations 5.6582294E-02 1.093095 at 100iterations 3.1487577E-02 0.5447845 at 110iterations 1.7423103E-02 0.3391190 at 120iterations 9.7010396E-03 0.1714692 at 130iterations 5.4339119E-03 0.1008606 at 140iterations 3.0842929E-03 6.6333771E-02 at 150iterations 1.7828285E-03 3.5884857E-02 at 160iterations 1.0720394E-03 2.3410797E-02 at 170iterations 6.8176730E-04 1.6029358E-02 at 180iterations finished qdiffx linear iterations at : 15:57:09 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 6.8176730E-04 1.6029358E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 15:57:10 12.804u 0.164s 0:13.25 97.8% 0+0k 0+0io 0pf+0w