Sat Oct 15 15:41:00 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 15 2011 at 15:41:00 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7289107 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): -14.59300 34.24700 ymin,ymax (A): -22.24800 24.71400 zmin,zma (A): -13.55900 28.55300 x,y,z range (A): 48.84000 46.96200 42.11200 scale (grids/A): 0.7289107 object centre (A): 9.827001 1.233000 7.497000 number of atom coordinates read : 2042 total number of charged atoms : 1926 net assigned charge : 5.851010 assigned positive charge : 315.5781 centred at (gu) : 89.48072 89.03759 90.13097 assigned negative charge : -309.7271 centred at (gu) : 89.58363 89.14916 90.20211 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7410 nv = 96 ne = 84 npr = 40655 no. pairs analyzed = 40655 no. exposed pairs = 2535 no. arc points = 17196 no. surface atoms = 860 nbur = 1182 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 550 mr = 4298 m= 3 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 3560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1536 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 8050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3146835E-07 2.4069363E-08 midg,1,midg; midg,igrid,midg 1.9898563E-07 -6.3288681E-09 1,midg,midg; igrid,midg,midg 1.7554785E-07 -1.0357281E-09 gauss-seidel spectral radius is 0.9901811 estimated iterations to convergence 82 setup time was (sec) 0.3500000 now iterating at: 15:41:01 rms-change max change #iterations 0.2308692 33.08112 at 10iterations 3.0209128E-02 4.417534 at 20iterations 4.2212494E-03 0.5316620 at 30iterations 6.9364806E-04 9.1970444E-02 at 40iterations 1.6775978E-04 2.2626877E-02 at 50iterations finished qdiffx linear iterations at : 15:41:05 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.6775978E-04 2.2626877E-02 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:41:06 3.614u 0.225s 0:05.87 65.2% 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 15 2011 at 15:41:06 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.186732 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): -14.59300 34.24700 ymin,ymax (A): -22.24800 24.71400 zmin,zma (A): -13.55900 28.55300 x,y,z range (A): 48.84000 46.96200 42.11200 scale (grids/A): 2.186732 object centre (A): 9.827001 1.233000 7.497000 number of atom coordinates read : 2042 total number of charged atoms : 1926 net assigned charge : 5.851010 assigned positive charge : 315.5781 centred at (gu) : 88.44222 87.11279 90.39288 assigned negative charge : -309.7271 centred at (gu) : 88.75101 87.44760 90.60637 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 78659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17196 grid for indexing accessible points = 1.400000 m= 32242 mr = 55864 m= 6445 mr = 24721 m= 635 mr = 4321 m= 19 mr = 349 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 32742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15311 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) : 0.7289107 object centre at (A) : 9.827001 1.233000 7.497000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4236349E-02 3.1378515E-02 midg,1,midg; midg,igrid,midg 5.5267062E-02 -5.9022095E-02 1,midg,midg; igrid,midg,midg 5.6162037E-02 2.8774507E-02 gauss-seidel spectral radius is 0.9988880 estimated iterations to convergence 237 setup time was (sec) 0.6400000 now iterating at: 15:41:07 rms-change max change #iterations 4.915697 215.0470 at 10iterations 2.470261 78.70804 at 20iterations 1.251865 42.63181 at 30iterations 0.6297073 17.29665 at 40iterations 0.3173878 9.445229 at 50iterations 0.1609986 4.531601 at 60iterations 8.1480697E-02 2.597757 at 70iterations 4.0983256E-02 1.176032 at 80iterations 2.0842150E-02 0.6086483 at 90iterations 1.0630601E-02 0.3260641 at 100iterations 5.4621929E-03 0.1555099 at 110iterations 2.8307098E-03 8.6359024E-02 at 120iterations finished qdiffx linear iterations at : 15:41:20 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 2.8307098E-03 8.6359024E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.530000 DelPhi exited at 15:41:21 8.528u 0.271s 0:14.74 59.6% 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 15 2011 at 15:41:21 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.280098 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): -14.59300 34.24700 ymin,ymax (A): -22.24800 24.71400 zmin,zma (A): -13.55900 28.55300 x,y,z range (A): 48.84000 46.96200 42.11200 scale (grids/A): 3.280098 object centre (A): 9.827001 1.233000 7.497000 number of atom coordinates read : 2042 total number of charged atoms : 1926 net assigned charge : 5.851010 assigned positive charge : 315.5781 centred at (gu) : 87.66325 85.66903 90.58942 assigned negative charge : -309.7271 centred at (gu) : 88.12660 86.17146 90.90965 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 181085 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17196 grid for indexing accessible points = 1.400000 m= 99872 mr = 134465 m= 41435 mr = 83467 m= 12245 mr = 34312 m= 2470 mr = 9566 m= 372 mr = 1760 m= 11 mr = 257 m= 0 mr = 5 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 73658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 15408 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) : 2.186732 object centre at (A) : 9.827001 1.233000 7.497000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1084949 0.2614744 midg,1,midg; midg,igrid,midg 0.4921724 -0.6832380 1,midg,midg; igrid,midg,midg 0.4227114 0.1704860 gauss-seidel spectral radius is 0.9993111 estimated iterations to convergence 301 setup time was (sec) 1.500000 now iterating at: 15:41:24 rms-change max change #iterations 10.73003 330.0623 at 10iterations 6.389916 121.9651 at 20iterations 3.792476 75.71017 at 30iterations 2.249299 43.80673 at 40iterations 1.333515 27.12144 at 50iterations 0.7863969 14.21378 at 60iterations 0.4646246 8.531023 at 70iterations 0.2747657 4.836647 at 80iterations 0.1619358 3.057159 at 90iterations 9.5675044E-02 1.762185 at 100iterations 5.6566089E-02 0.9234858 at 110iterations 3.3554524E-02 0.5890579 at 120iterations 2.0006925E-02 0.3997040 at 130iterations 1.2133782E-02 0.2246017 at 140iterations 7.5265733E-03 0.1278858 at 150iterations 4.8406529E-03 9.3872070E-02 at 160iterations 3.2617415E-03 6.2305450E-02 at 170iterations 2.3339172E-03 4.1755676E-02 at 180iterations finished qdiffx linear iterations at : 15:41:43 total time elapsed so far: 13.90000 # loops : 180 mean,max change (kT/e) : 2.3339172E-03 4.1755676E-02 energy calculations done at 13.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.04000 DelPhi exited at 15:41:43 14.040u 0.303s 0:21.97 65.2% 0+0k 0+0io 0pf+0w