Wed Dec 28 11:03:04 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 11:03:05 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: 235 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 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: 0.5922180 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): -20.00900 40.10400 ymin,ymax (A): -17.64000 25.02100 zmin,zma (A): -18.31800 23.83900 x,y,z range (A): 60.11300 42.66100 42.15700 scale (grids/A): 0.5922180 object centre (A): 10.04750 3.690500 2.760499 number of atom coordinates read : 1952 total number of charged atoms : 1818 net assigned charge : -1.999994 assigned positive charge : 292.0978 centred at (gu) : 91.52853 89.29128 89.77940 assigned negative charge : -294.0981 centred at (gu) : 91.50924 89.27917 89.88432 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4542 nv = 96 ne = 84 npr = 39637 no. pairs analyzed = 39637 no. exposed pairs = 2518 no. arc points = 17505 no. surface atoms = 855 nbur = 1097 mkacc time = 0.1000000 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= 203 mr = 2433 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1788 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 5638 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6531234E-09 -2.8170646E-09 midg,1,midg; midg,igrid,midg -1.0943620E-09 -3.5165615E-10 1,midg,midg; igrid,midg,midg -7.7150070E-10 -3.4820624E-10 gauss-seidel spectral radius is 0.9851928 estimated iterations to convergence 67 setup time was (sec) 0.7600000 now iterating at: 11:03:06 rms-change max change #iterations 8.9339897E-02 15.22607 at 10iterations 7.3133791E-03 1.271351 at 20iterations 6.0068758E-04 0.1023407 at 30iterations 4.8667836E-05 7.5149536E-03 at 40iterations 3.8862140E-06 6.8092346E-04 at 50iterations finished qdiffx linear iterations at : 11:03:13 total time elapsed so far: 7.750000 # loops : 50 mean,max change (kT/e) : 3.8862140E-06 6.8092346E-04 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 11:03:14 7.964u 0.681s 0:09.08 95.1% 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 11:03:14 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: 235 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 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: 1.776654 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): -20.00900 40.10400 ymin,ymax (A): -17.64000 25.02100 zmin,zma (A): -18.31800 23.83900 x,y,z range (A): 60.11300 42.66100 42.15700 scale (grids/A): 1.776654 object centre (A): 10.04750 3.690500 2.760499 number of atom coordinates read : 1952 total number of charged atoms : 1818 net assigned charge : -1.999994 assigned positive charge : 292.0978 centred at (gu) : 94.58552 87.87371 89.33811 assigned negative charge : -294.0981 centred at (gu) : 94.52779 87.83749 89.65292 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 49548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17505 grid for indexing accessible points = 1.400000 m= 16736 mr = 33481 m= 2159 mr = 12321 m= 93 mr = 1281 m= 0 mr = 29 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 339 time to turn everything in is 0.4800000 number of dielectric boundary points 21424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14159 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) : 0.5922180 object centre at (A) : 10.04750 3.690500 2.760499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3996203E-03 -6.2042880E-03 midg,1,midg; midg,igrid,midg -7.6050670E-03 -8.4859682E-03 1,midg,midg; igrid,midg,midg 3.1676290E-03 9.5851161E-03 gauss-seidel spectral radius is 0.9983531 estimated iterations to convergence 196 setup time was (sec) 0.9900000 now iterating at: 11:03:15 rms-change max change #iterations 3.177444 161.2015 at 10iterations 1.373963 61.60159 at 20iterations 0.5978492 25.02394 at 30iterations 0.2595481 10.53095 at 40iterations 0.1122740 4.407402 at 50iterations 4.8667856E-02 1.891465 at 60iterations 2.1232959E-02 0.8535271 at 70iterations 9.2117107E-03 0.3476105 at 80iterations 3.9957175E-03 0.1679809 at 90iterations 1.7339682E-03 6.4994812E-02 at 100iterations 7.5486751E-04 2.9746771E-02 at 110iterations 3.2769743E-04 1.3080835E-02 at 120iterations finished qdiffx linear iterations at : 11:03:32 total time elapsed so far: 17.47000 # loops : 120 mean,max change (kT/e) : 3.2769743E-04 1.3080835E-02 energy calculations done at 17.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.64000 DelPhi exited at 11:03:34 17.646u 0.815s 0:20.09 91.8% 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 Wed Dec 28 2011 at 11:03:34 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: 235 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 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: 2.664981 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): -20.00900 40.10400 ymin,ymax (A): -17.64000 25.02100 zmin,zma (A): -18.31800 23.83900 x,y,z range (A): 60.11300 42.66100 42.15700 scale (grids/A): 2.664981 object centre (A): 10.04750 3.690500 2.760499 number of atom coordinates read : 1952 total number of charged atoms : 1818 net assigned charge : -1.999994 assigned positive charge : 292.0978 centred at (gu) : 96.87832 86.81051 89.00720 assigned negative charge : -294.0981 centred at (gu) : 96.79173 86.75626 89.47940 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 114733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17505 grid for indexing accessible points = 1.400000 m= 55559 mr = 81562 m= 18342 mr = 45099 m= 3623 mr = 14751 m= 426 mr = 2671 m= 28 mr = 272 m= 0 mr = 8 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1200 time to turn everything in is 1.160000 number of dielectric boundary points 48348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 14543 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) : 1.776654 object centre at (A) : 10.04750 3.690500 2.760499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7740165E-02 -8.0404796E-02 midg,1,midg; midg,igrid,midg -6.9109425E-02 -0.1088953 1,midg,midg; igrid,midg,midg 7.3456317E-02 0.3264885 gauss-seidel spectral radius is 0.9991604 estimated iterations to convergence 273 setup time was (sec) 1.660000 now iterating at: 11:03:36 rms-change max change #iterations 7.669720 291.8421 at 10iterations 4.302690 101.2413 at 20iterations 2.386292 61.62515 at 30iterations 1.320232 34.37511 at 40iterations 0.7350059 16.41190 at 50iterations 0.4059663 9.325298 at 60iterations 0.2245385 4.817683 at 70iterations 0.1242852 2.930533 at 80iterations 6.8692394E-02 1.518138 at 90iterations 3.7998103E-02 0.9294815 at 100iterations 2.1008981E-02 0.4953957 at 110iterations 1.1612099E-02 0.2567253 at 120iterations 6.4028348E-03 0.1426871 at 130iterations 3.5475264E-03 8.4769011E-02 at 140iterations 1.9590931E-03 4.2632580E-02 at 150iterations 1.0825159E-03 2.6646614E-02 at 160iterations 5.9844187E-04 1.3237000E-02 at 170iterations 3.3111533E-04 7.6732635E-03 at 180iterations finished qdiffx linear iterations at : 11:04:01 total time elapsed so far: 26.21000 # loops : 180 mean,max change (kT/e) : 3.3111533E-04 7.6732635E-03 energy calculations done at 26.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 26.40000 DelPhi exited at 11:04:02 26.409u 0.793s 0:27.91 97.4% 0+0k 0+0io 0pf+0w