Sun Oct 9 15:15:03 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 Sun Oct 9 2011 at 15:15:03 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 = 5385 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: 0.5127023 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): -16.49900 52.93700 ymin,ymax (A): 97.20100 163.8320 zmin,zma (A): -29.89800 31.82400 x,y,z range (A): 69.43600 66.63100 61.72200 scale (grids/A): 0.5127023 object centre (A): 18.21900 130.5165 0.9630003 number of atom coordinates read : 5385 total number of charged atoms : 5214 net assigned charge : -5.499960 assigned positive charge : 820.8727 centred at (gu) : 89.42484 89.02958 88.43922 assigned negative charge : -826.3792 centred at (gu) : 89.45906 89.11282 88.38203 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8655 nv = 96 ne = 84 npr = 111939 no. pairs analyzed = 111939 no. exposed pairs = 6268 no. arc points = 43589 no. surface atoms = 2099 nbur = 3286 mkacc time = 0.2400000 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 = 1.680000 m= 300 mr = 4724 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.4800000 number of dielectric boundary points 4228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4246 ## 611 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 11865 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1470039E-10 6.5093694E-11 midg,1,midg; midg,igrid,midg 2.3921548E-10 -2.7965300E-10 1,midg,midg; igrid,midg,midg 3.0646565E-11 -1.7041722E-10 gauss-seidel spectral radius is 0.9805750 estimated iterations to convergence 59 setup time was (sec) 0.6900000 now iterating at: 15:15:04 rms-change max change #iterations 7.2863542E-02 12.69972 at 10iterations 4.4149975E-03 0.5984573 at 20iterations 4.0152192E-04 5.3683281E-02 at 30iterations 7.7469296E-05 1.1289597E-02 at 40iterations 1.8119877E-05 2.5300980E-03 at 50iterations finished qdiffx linear iterations at : 15:15:06 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.8119877E-05 2.5300980E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 15:15:07 3.330u 0.160s 0:03.84 90.8% 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 15:15:07 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 = 5385 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: 1.538107 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): -16.49900 52.93700 ymin,ymax (A): 97.20100 163.8320 zmin,zma (A): -29.89800 31.82400 x,y,z range (A): 69.43600 66.63100 61.72200 scale (grids/A): 1.538107 object centre (A): 18.21900 130.5165 0.9630003 number of atom coordinates read : 5385 total number of charged atoms : 5214 net assigned charge : -5.499960 assigned positive charge : 820.8727 centred at (gu) : 88.27274 87.08677 85.31594 assigned negative charge : -826.3792 centred at (gu) : 88.37695 87.33829 85.14595 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 99082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43589 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 28540 mr = 70001 m= 2412 mr = 19539 m= 53 mr = 1070 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3449 time to turn everything in is 0.6600000 number of dielectric boundary points 39477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 525 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 39123 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) : 0.5127023 object centre at (A) : 18.21900 130.5165 0.9630003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0521591E-03 -5.2241203E-03 midg,1,midg; midg,igrid,midg 1.4554300E-02 -1.7065138E-02 1,midg,midg; igrid,midg,midg -2.7627800E-02 -4.8551061E-03 gauss-seidel spectral radius is 0.9981692 estimated iterations to convergence 186 setup time was (sec) 0.9400000 now iterating at: 15:15:08 rms-change max change #iterations 4.136185 153.1882 at 10iterations 1.717083 58.85973 at 20iterations 0.7162923 23.71926 at 30iterations 0.2985734 10.04316 at 40iterations 0.1245931 3.662527 at 50iterations 5.1545829E-02 1.615204 at 60iterations 2.1639455E-02 0.6850252 at 70iterations 9.0230191E-03 0.2689880 at 80iterations 3.7581208E-03 0.1074662 at 90iterations 1.5760448E-03 4.5275688E-02 at 100iterations 6.6020479E-04 2.0174026E-02 at 110iterations 2.7783890E-04 8.4381104E-03 at 120iterations finished qdiffx linear iterations at : 15:15:14 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 2.7783890E-04 8.4381104E-03 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.200000 DelPhi exited at 15:15:15 7.200u 0.164s 0:07.66 96.0% 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 Sun Oct 9 2011 at 15:15:15 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 = 5385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.307160 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): -16.49900 52.93700 ymin,ymax (A): 97.20100 163.8320 zmin,zma (A): -29.89800 31.82400 x,y,z range (A): 69.43600 66.63100 61.72200 scale (grids/A): 2.307160 object centre (A): 18.21900 130.5165 0.9630003 number of atom coordinates read : 5385 total number of charged atoms : 5214 net assigned charge : -5.499960 assigned positive charge : 820.8727 centred at (gu) : 87.40879 85.62975 82.97366 assigned negative charge : -826.3792 centred at (gu) : 87.56538 86.00721 82.71907 start vw surface at 0.2100000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 231647 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43589 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 102996 mr = 172181 m= 26009 mr = 81609 m= 3644 mr = 19251 m= 203 mr = 2317 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 12137 time to turn everything in is 1.560000 number of dielectric boundary points 89084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 41601 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) : 1.538107 object centre at (A) : 18.21900 130.5165 0.9630003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9497416E-03 -0.1438833 midg,1,midg; midg,igrid,midg 0.2655685 -0.3813155 1,midg,midg; igrid,midg,midg -0.3613681 1.5613729E-02 gauss-seidel spectral radius is 0.9991839 estimated iterations to convergence 276 setup time was (sec) 1.840000 now iterating at: 15:15:17 rms-change max change #iterations 11.06264 318.1917 at 10iterations 6.330926 140.8061 at 20iterations 3.597778 73.34863 at 30iterations 2.038975 41.12774 at 40iterations 1.151322 25.64414 at 50iterations 0.6488315 11.42709 at 60iterations 0.3646811 7.986927 at 70iterations 0.2052373 3.499313 at 80iterations 0.1150006 2.266586 at 90iterations 6.4502932E-02 1.150944 at 100iterations 3.6076732E-02 0.6395454 at 110iterations 2.0217104E-02 0.3980427 at 120iterations 1.1313054E-02 0.1941166 at 130iterations 6.3368110E-03 0.1061707 at 140iterations 3.5463918E-03 5.7174683E-02 at 150iterations 1.9852251E-03 3.4329414E-02 at 160iterations 1.1114971E-03 1.8542528E-02 at 170iterations 6.2312168E-04 1.0971069E-02 at 180iterations finished qdiffx linear iterations at : 15:15:26 total time elapsed so far: 11.46000 # loops : 180 mean,max change (kT/e) : 6.2312168E-04 1.0971069E-02 energy calculations done at 11.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 15:15:27 11.636u 0.183s 0:12.12 97.4% 0+0k 0+0io 0pf+0w