Tue Oct 11 07:07:30 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 Tue Oct 11 2011 at 07:07:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3475 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: 0.5583525 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): -110.9330 -55.76000 ymin,ymax (A): -45.50300 18.25600 zmin,zma (A): 9.485000 66.91700 x,y,z range (A): 55.17300 63.75900 57.43200 scale (grids/A): 0.5583525 object centre (A): -83.34650 -13.62350 38.20100 number of atom coordinates read : 3475 total number of charged atoms : 3334 net assigned charge : 4.000016 assigned positive charge : 522.7937 centred at (gu) : 88.95667 91.34084 88.95380 assigned negative charge : -518.7957 centred at (gu) : 89.01348 91.44003 89.16328 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6894 nv = 96 ne = 84 npr = 70583 no. pairs analyzed = 70583 no. exposed pairs = 4320 no. arc points = 29322 no. surface atoms = 1476 nbur = 1999 mkacc time = 0.1200000 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 = 1.540000 m= 324 mr = 3653 m= 0 mr = 44 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3025 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9086 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7025434E-09 -1.7197217E-09 midg,1,midg; midg,igrid,midg 1.1367137E-09 -1.1778203E-09 1,midg,midg; igrid,midg,midg 1.3764153E-09 -2.3825944E-10 gauss-seidel spectral radius is 0.9834896 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 07:07:30 rms-change max change #iterations 8.9702547E-02 12.86682 at 10iterations 7.5677368E-03 1.099628 at 20iterations 1.0910990E-03 0.1774216 at 30iterations 2.5727806E-04 4.1877747E-02 at 40iterations 6.7456378E-05 1.0993958E-02 at 50iterations finished qdiffx linear iterations at : 07:07:33 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 6.7456378E-05 1.0993958E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 07:07:34 3.397u 0.160s 0:04.08 87.0% 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 Tue Oct 11 2011 at 07:07:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3475 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: 1.675058 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): -110.9330 -55.76000 ymin,ymax (A): -45.50300 18.25600 zmin,zma (A): 9.485000 66.91700 x,y,z range (A): 55.17300 63.75900 57.43200 scale (grids/A): 1.675058 object centre (A): -83.34650 -13.62350 38.20100 number of atom coordinates read : 3475 total number of charged atoms : 3334 net assigned charge : 4.000016 assigned positive charge : 522.7937 centred at (gu) : 86.86873 94.02109 86.86013 assigned negative charge : -518.7957 centred at (gu) : 87.03998 94.31982 87.48932 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 74861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29322 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25511 mr = 51087 m= 3299 mr = 18202 m= 117 mr = 1860 m= 4 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 161 time to turn everything in is 0.3800000 number of dielectric boundary points 32627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 25729 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) : 0.5583525 object centre at (A) : -83.34650 -13.62350 38.20100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1376938E-02 -4.6521012E-02 midg,1,midg; midg,igrid,midg 3.2772955E-02 -1.6161083E-04 1,midg,midg; igrid,midg,midg 7.5563428E-04 -3.4350718E-04 gauss-seidel spectral radius is 0.9983219 estimated iterations to convergence 194 setup time was (sec) 0.5900000 now iterating at: 07:07:35 rms-change max change #iterations 3.837384 216.4542 at 10iterations 1.655359 69.52754 at 20iterations 0.7131404 23.58795 at 30iterations 0.3082224 11.13571 at 40iterations 0.1335375 4.195415 at 50iterations 5.7774037E-02 1.987450 at 60iterations 2.5090929E-02 0.8085747 at 70iterations 1.0992256E-02 0.3696861 at 80iterations 4.8941309E-03 0.1675644 at 90iterations 2.2213780E-03 8.3854675E-02 at 100iterations 1.0578061E-03 3.7311554E-02 at 110iterations 5.3583900E-04 2.0095825E-02 at 120iterations finished qdiffx linear iterations at : 07:07:42 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 5.3583900E-04 2.0095825E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 07:07:42 7.688u 0.196s 0:08.43 93.3% 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 Tue Oct 11 2011 at 07:07:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3475 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: 2.512586 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): -110.9330 -55.76000 ymin,ymax (A): -45.50300 18.25600 zmin,zma (A): 9.485000 66.91700 x,y,z range (A): 55.17300 63.75900 57.43200 scale (grids/A): 2.512586 object centre (A): -83.34650 -13.62350 38.20100 number of atom coordinates read : 3475 total number of charged atoms : 3334 net assigned charge : 4.000016 assigned positive charge : 522.7937 centred at (gu) : 85.30281 96.03146 85.28987 assigned negative charge : -518.7957 centred at (gu) : 85.55999 96.47958 86.23395 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 173772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29322 grid for indexing accessible points = 1.400000 m= 84032 mr = 124863 m= 28223 mr = 67031 m= 5575 mr = 22287 m= 478 mr = 3932 m= 3 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 620 time to turn everything in is 0.9500000 number of dielectric boundary points 73729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 26651 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) : 1.675058 object centre at (A) : -83.34650 -13.62350 38.20100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2908449 -0.8780429 midg,1,midg; midg,igrid,midg 0.6192357 -0.1594608 1,midg,midg; igrid,midg,midg -5.0983485E-02 -8.1983292E-03 gauss-seidel spectral radius is 0.9991879 estimated iterations to convergence 277 setup time was (sec) 1.180000 now iterating at: 07:07:44 rms-change max change #iterations 9.791326 281.2807 at 10iterations 5.615419 210.4050 at 20iterations 3.204500 86.22177 at 30iterations 1.819659 34.85928 at 40iterations 1.030108 24.25900 at 50iterations 0.5796502 11.28323 at 60iterations 0.3268724 6.243799 at 70iterations 0.1840080 3.377230 at 80iterations 0.1032643 2.052902 at 90iterations 5.7950910E-02 1.165276 at 100iterations 3.2520823E-02 0.5909462 at 110iterations 1.8314619E-02 0.3500724 at 120iterations 1.0331190E-02 0.2359076 at 130iterations 5.8383867E-03 0.1092224 at 140iterations 3.3240281E-03 6.4613342E-02 at 150iterations 1.9239205E-03 3.8176537E-02 at 160iterations 1.1323785E-03 2.5875092E-02 at 170iterations 6.8851636E-04 1.4728546E-02 at 180iterations finished qdiffx linear iterations at : 07:07:55 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 6.8851636E-04 1.4728546E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 07:07:56 12.706u 0.206s 0:13.31 96.9% 0+0k 0+0io 0pf+0w