Mon Oct 10 17:03:08 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 Mon Oct 10 2011 at 17:03:08 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 = 2779 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: 0.5646312 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): -35.35500 9.116000 ymin,ymax (A): -31.81000 31.24000 zmin,zma (A): -24.11400 23.12400 x,y,z range (A): 44.47100 63.05000 47.23800 scale (grids/A): 0.5646312 object centre (A): -13.11950 -0.2849998 -0.4949999 number of atom coordinates read : 2779 total number of charged atoms : 2640 net assigned charge : -1.499972 assigned positive charge : 415.1733 centred at (gu) : 90.28545 90.16361 90.88485 assigned negative charge : -416.6744 centred at (gu) : 90.45591 90.11726 91.05017 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5846 nv = 96 ne = 84 npr = 54921 no. pairs analyzed = 54921 no. exposed pairs = 3661 no. arc points = 26013 no. surface atoms = 1227 nbur = 1552 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= 243 mr = 2958 m= 1 mr = 12 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 0.2800000 number of dielectric boundary points 3120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2688 ## 350 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7573 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4666831E-09 -2.7583675E-09 midg,1,midg; midg,igrid,midg -7.0106165E-10 4.2039774E-10 1,midg,midg; igrid,midg,midg 1.7533924E-09 -2.4512545E-09 gauss-seidel spectral radius is 0.9838065 estimated iterations to convergence 65 setup time was (sec) 0.4900000 now iterating at: 17:03:09 rms-change max change #iterations 8.1989191E-02 12.58978 at 10iterations 5.9924698E-03 1.161041 at 20iterations 4.3695138E-04 6.7749500E-02 at 30iterations 3.1338255E-05 5.4454803E-03 at 40iterations 2.3656155E-06 3.7384033E-04 at 50iterations finished qdiffx linear iterations at : 17:03:11 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.3656155E-06 3.7384033E-04 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 17:03:12 3.086u 0.151s 0:03.57 90.4% 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 Mon Oct 10 2011 at 17:03:12 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 = 2779 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.693894 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): -35.35500 9.116000 ymin,ymax (A): -31.81000 31.24000 zmin,zma (A): -24.11400 23.12400 x,y,z range (A): 44.47100 63.05000 47.23800 scale (grids/A): 1.693894 object centre (A): -13.11950 -0.2849998 -0.4949999 number of atom coordinates read : 2779 total number of charged atoms : 2640 net assigned charge : -1.499972 assigned positive charge : 415.1733 centred at (gu) : 90.85580 90.49001 92.65372 assigned negative charge : -416.6744 centred at (gu) : 91.36710 90.35183 93.15019 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64660 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26013 grid for indexing accessible points = 1.400000 m= 19495 mr = 43110 m= 2018 mr = 13221 m= 48 mr = 1015 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.4400000 number of dielectric boundary points 28870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 20359 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) : 0.5646312 object centre at (A) : -13.11950 -0.2849998 -0.4949999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8942279E-03 -1.9622294E-02 midg,1,midg; midg,igrid,midg 4.4977342E-04 5.7038702E-03 1,midg,midg; igrid,midg,midg 5.2223094E-03 -7.5438716E-03 gauss-seidel spectral radius is 0.9983001 estimated iterations to convergence 193 setup time was (sec) 0.7100000 now iterating at: 17:03:13 rms-change max change #iterations 3.458207 154.2305 at 10iterations 1.478819 57.21605 at 20iterations 0.6379270 24.33937 at 30iterations 0.2724827 11.06786 at 40iterations 0.1169066 4.443226 at 50iterations 5.0215632E-02 1.671600 at 60iterations 2.1509912E-02 0.7643566 at 70iterations 9.2185270E-03 0.3649826 at 80iterations 3.9471779E-03 0.1453428 at 90iterations 1.6988050E-03 6.4590454E-02 at 100iterations 7.2554196E-04 2.5988579E-02 at 110iterations 3.1251559E-04 1.1238098E-02 at 120iterations finished qdiffx linear iterations at : 17:03:19 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 3.1251559E-04 1.1238098E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 17:03:21 7.015u 0.172s 0:09.20 78.0% 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 Mon Oct 10 2011 at 17:03:21 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 = 2779 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.540841 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): -35.35500 9.116000 ymin,ymax (A): -31.81000 31.24000 zmin,zma (A): -24.11400 23.12400 x,y,z range (A): 44.47100 63.05000 47.23800 scale (grids/A): 2.540841 object centre (A): -13.11950 -0.2849998 -0.4949999 number of atom coordinates read : 2779 total number of charged atoms : 2640 net assigned charge : -1.499972 assigned positive charge : 415.1733 centred at (gu) : 91.28355 90.73484 93.98032 assigned negative charge : -416.6744 centred at (gu) : 92.05054 90.52771 94.72530 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 150057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26013 grid for indexing accessible points = 1.400000 m= 67513 mr = 105576 m= 18958 mr = 52732 m= 3086 mr = 14203 m= 237 mr = 2070 m= 8 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1072 time to turn everything in is 1.050000 number of dielectric boundary points 65183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 21105 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) : 1.693894 object centre at (A) : -13.11950 -0.2849998 -0.4949999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5746510E-02 -0.2414708 midg,1,midg; midg,igrid,midg 0.4203501 0.1037864 1,midg,midg; igrid,midg,midg 4.9794868E-02 -8.8203713E-02 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.330000 now iterating at: 17:03:23 rms-change max change #iterations 8.874589 328.9989 at 10iterations 5.041343 122.9577 at 20iterations 2.857062 74.26361 at 30iterations 1.608618 39.30527 at 40iterations 0.9035594 20.91711 at 50iterations 0.5064707 10.90009 at 60iterations 0.2837011 6.481238 at 70iterations 0.1585485 3.539617 at 80iterations 8.8614337E-02 1.969553 at 90iterations 4.9397744E-02 1.052467 at 100iterations 2.7550932E-02 0.5548069 at 110iterations 1.5303345E-02 0.2956705 at 120iterations 8.5537294E-03 0.1791725 at 130iterations 4.7690994E-03 9.8148346E-02 at 140iterations 2.6545064E-03 5.5073738E-02 at 150iterations 1.4779289E-03 2.9847622E-02 at 160iterations 8.2471094E-04 1.7826080E-02 at 170iterations 4.5883833E-04 9.6435547E-03 at 180iterations finished qdiffx linear iterations at : 17:03:32 total time elapsed so far: 11.03000 # loops : 180 mean,max change (kT/e) : 4.5883833E-04 9.6435547E-03 energy calculations done at 11.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.19000 DelPhi exited at 17:03:33 11.194u 0.167s 0:11.72 96.8% 0+0k 0+0io 0pf+0w