Sat Oct 8 14:03:35 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 Sat Oct 8 2011 at 14:03:35 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6404721 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): -12.43700 43.14700 ymin,ymax (A): -22.34500 22.54200 zmin,zma (A): -7.244000 47.32200 x,y,z range (A): 55.58400 44.88700 54.56600 scale (grids/A): 0.6404721 object centre (A): 15.35500 9.8499298E-02 20.03900 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 1.4008060E-02 assigned positive charge : 457.8656 centred at (gu) : 88.73769 89.55670 91.61784 assigned negative charge : -457.8523 centred at (gu) : 88.73243 89.46307 91.53220 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8238 nv = 96 ne = 84 npr = 64188 no. pairs analyzed = 64188 no. exposed pairs = 3449 no. arc points = 23913 no. surface atoms = 1179 nbur = 1864 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 4826 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2375 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5345295E-09 1.6660712E-08 midg,1,midg; midg,igrid,midg -1.4584622E-08 1.1581150E-08 1,midg,midg; igrid,midg,midg -1.1074762E-09 4.7215365E-10 gauss-seidel spectral radius is 0.9874004 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 14:03:36 rms-change max change #iterations 0.1623295 25.59786 at 10iterations 1.6796742E-02 2.208046 at 20iterations 1.7340349E-03 0.2646866 at 30iterations 2.1413621E-04 2.6969910E-02 at 40iterations 3.3114742E-05 4.1656494E-03 at 50iterations finished qdiffx linear iterations at : 14:03:40 total time elapsed so far: 4.680000 # loops : 50 mean,max change (kT/e) : 3.3114742E-05 4.1656494E-03 energy calculations done at 4.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.840000 DelPhi exited at 14:03:40 4.843u 0.385s 0:05.49 95.0% 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 Sat Oct 8 2011 at 14:03:40 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.921416 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): -12.43700 43.14700 ymin,ymax (A): -22.34500 22.54200 zmin,zma (A): -7.244000 47.32200 x,y,z range (A): 55.58400 44.88700 54.56600 scale (grids/A): 1.921416 object centre (A): 15.35500 9.8499298E-02 20.03900 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 1.4008060E-02 assigned positive charge : 457.8656 centred at (gu) : 86.21254 88.66974 94.85284 assigned negative charge : -457.8523 centred at (gu) : 86.19694 88.38902 94.59634 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23913 grid for indexing accessible points = 1.400000 m= 32384 mr = 65117 m= 4703 mr = 24333 m= 277 mr = 2849 m= 5 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 170 time to turn everything in is 0.7100000 number of dielectric boundary points 34785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22824 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) : 0.6404721 object centre at (A) : 15.35500 9.8499298E-02 20.03900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4792470E-02 2.6134897E-02 midg,1,midg; midg,igrid,midg -2.5181149E-03 1.6666146E-02 1,midg,midg; igrid,midg,midg -3.5468072E-02 1.1461074E-02 gauss-seidel spectral radius is 0.9986913 estimated iterations to convergence 219 setup time was (sec) 1.010000 now iterating at: 14:03:42 rms-change max change #iterations 4.753825 172.5606 at 10iterations 2.270261 62.76699 at 20iterations 1.081836 32.36460 at 30iterations 0.5160847 15.08914 at 40iterations 0.2456503 7.020392 at 50iterations 0.1174429 3.484188 at 60iterations 5.5850357E-02 1.578856 at 70iterations 2.6640076E-02 0.7901115 at 80iterations 1.2713141E-02 0.3596420 at 90iterations 6.0741161E-03 0.1823673 at 100iterations 2.9009709E-03 8.5701227E-02 at 110iterations 1.3884922E-03 4.2495728E-02 at 120iterations finished qdiffx linear iterations at : 14:03:51 total time elapsed so far: 10.82000 # loops : 120 mean,max change (kT/e) : 1.3884922E-03 4.2495728E-02 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.99000 DelPhi exited at 14:03:52 10.993u 0.431s 0:11.69 97.6% 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 Sat Oct 8 2011 at 14:03:52 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.882124 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): -12.43700 43.14700 ymin,ymax (A): -22.34500 22.54200 zmin,zma (A): -7.244000 47.32200 x,y,z range (A): 55.58400 44.88700 54.56600 scale (grids/A): 2.882124 object centre (A): 15.35500 9.8499298E-02 20.03900 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 1.4008060E-02 assigned positive charge : 457.8656 centred at (gu) : 84.31880 88.00447 97.27920 assigned negative charge : -457.8523 centred at (gu) : 84.29539 87.58340 96.89446 start vw surface at 0.1300000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 208138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23913 grid for indexing accessible points = 1.400000 m= 106535 mr = 157204 m= 36996 mr = 88863 m= 8318 mr = 29876 m= 1188 mr = 6066 m= 86 mr = 781 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 595 time to turn everything in is 1.990000 number of dielectric boundary points 78444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 23167 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) : 1.921416 object centre at (A) : 15.35500 9.8499298E-02 20.03900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1204680 0.5580207 midg,1,midg; midg,igrid,midg -2.6307287E-02 0.2016254 1,midg,midg; igrid,midg,midg -0.6102863 0.1660711 gauss-seidel spectral radius is 0.9992769 estimated iterations to convergence 293 setup time was (sec) 2.330000 now iterating at: 14:03:55 rms-change max change #iterations 11.05765 376.0115 at 10iterations 6.508215 131.1146 at 20iterations 3.812303 67.61414 at 30iterations 2.229568 43.79274 at 40iterations 1.296144 22.08755 at 50iterations 0.7576219 12.41948 at 60iterations 0.4401243 7.949989 at 70iterations 0.2555810 4.357616 at 80iterations 0.1482202 2.382523 at 90iterations 8.5997954E-02 1.560362 at 100iterations 4.9769469E-02 0.8274012 at 110iterations 2.8882412E-02 0.4945641 at 120iterations 1.6808134E-02 0.2903824 at 130iterations 9.7371098E-03 0.1602020 at 140iterations 5.6597437E-03 0.1006021 at 150iterations 3.2885913E-03 5.2665710E-02 at 160iterations 1.9184985E-03 3.2153130E-02 at 170iterations 1.1262626E-03 1.9062042E-02 at 180iterations finished qdiffx linear iterations at : 14:04:12 total time elapsed so far: 20.07000 # loops : 180 mean,max change (kT/e) : 1.1262626E-03 1.9062042E-02 energy calculations done at 20.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.24000 DelPhi exited at 14:04:13 20.242u 0.477s 0:20.99 98.6% 0+0k 0+0io 0pf+0w