Tue Oct 11 01:12:51 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 Tue Oct 11 2011 at 01:12:51 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6095995 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): -5.162000 53.23700 ymin,ymax (A): -15.92000 29.99800 zmin,zma (A): 57.25100 109.3970 x,y,z range (A): 58.39900 45.91800 52.14600 scale (grids/A): 0.6095995 object centre (A): 24.03750 7.039001 83.32401 number of atom coordinates read : 2814 total number of charged atoms : 2661 net assigned charge : 5.312018 assigned positive charge : 426.6425 centred at (gu) : 89.55669 90.14509 89.44070 assigned negative charge : -421.3311 centred at (gu) : 89.78310 90.07417 89.46935 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6897 nv = 96 ne = 84 npr = 57166 no. pairs analyzed = 57166 no. exposed pairs = 3295 no. arc points = 23134 no. surface atoms = 1117 nbur = 1697 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3902 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 0.3500000 number of dielectric boundary points 3262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2373 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8589 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1519984E-09 1.3481981E-09 midg,1,midg; midg,igrid,midg -7.3007378E-10 6.9955690E-09 1,midg,midg; igrid,midg,midg 1.6311503E-08 -8.3955136E-09 gauss-seidel spectral radius is 0.9860832 estimated iterations to convergence 69 setup time was (sec) 0.6200000 now iterating at: 01:12:52 rms-change max change #iterations 0.1240541 18.12474 at 10iterations 1.1572102E-02 1.979462 at 20iterations 1.4174972E-03 0.2628059 at 30iterations 2.8910537E-04 6.7893982E-02 at 40iterations 7.5634220E-05 1.8177032E-02 at 50iterations finished qdiffx linear iterations at : 01:12:55 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 7.5634220E-05 1.8177032E-02 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 01:12:56 4.148u 0.291s 0:04.75 93.2% 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 Tue Oct 11 2011 at 01:12:56 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.828798 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): -5.162000 53.23700 ymin,ymax (A): -15.92000 29.99800 zmin,zma (A): 57.25100 109.3970 x,y,z range (A): 58.39900 45.91800 52.14600 scale (grids/A): 1.828798 object centre (A): 24.03750 7.039001 83.32401 number of atom coordinates read : 2814 total number of charged atoms : 2661 net assigned charge : 5.312018 assigned positive charge : 426.6425 centred at (gu) : 88.66949 90.43452 88.32118 assigned negative charge : -421.3311 centred at (gu) : 89.34883 90.22211 88.40761 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23134 grid for indexing accessible points = 1.400000 m= 26049 mr = 53083 m= 3575 mr = 19352 m= 173 mr = 2307 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 7350 time to turn everything in is 0.6500000 number of dielectric boundary points 30286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20819 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) : 0.6095995 object centre at (A) : 24.03750 7.039001 83.32401 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7855631E-03 5.0718263E-03 midg,1,midg; midg,igrid,midg 9.9122683E-03 1.3484046E-02 1,midg,midg; igrid,midg,midg 4.7369029E-02 -1.6196063E-02 gauss-seidel spectral radius is 0.9985385 estimated iterations to convergence 207 setup time was (sec) 0.9500000 now iterating at: 01:12:57 rms-change max change #iterations 4.174349 186.3471 at 10iterations 1.899981 62.72626 at 20iterations 0.8656655 28.60461 at 30iterations 0.3959112 14.56492 at 40iterations 0.1802550 5.320141 at 50iterations 8.2470633E-02 2.729458 at 60iterations 3.7794366E-02 1.148983 at 70iterations 1.7383398E-02 0.5763087 at 80iterations 8.0403369E-03 0.2650108 at 90iterations 3.7836763E-03 0.1371918 at 100iterations 1.8188375E-03 6.6898346E-02 at 110iterations 9.1770152E-04 4.0802002E-02 at 120iterations finished qdiffx linear iterations at : 01:13:05 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 9.1770152E-04 4.0802002E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 01:13:06 9.532u 0.329s 0:10.37 94.9% 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 Tue Oct 11 2011 at 01:13:06 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.743197 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): -5.162000 53.23700 ymin,ymax (A): -15.92000 29.99800 zmin,zma (A): 57.25100 109.3970 x,y,z range (A): 58.39900 45.91800 52.14600 scale (grids/A): 2.743197 object centre (A): 24.03750 7.039001 83.32401 number of atom coordinates read : 2814 total number of charged atoms : 2661 net assigned charge : 5.312018 assigned positive charge : 426.6425 centred at (gu) : 88.00386 90.65160 87.48178 assigned negative charge : -421.3311 centred at (gu) : 89.02325 90.33299 87.61134 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 174797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23134 grid for indexing accessible points = 1.400000 m= 86318 mr = 128751 m= 28986 mr = 71185 m= 6496 mr = 23489 m= 752 mr = 5031 m= 26 mr = 511 m= 0 mr = 11 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 24837 time to turn everything in is 1.650000 number of dielectric boundary points 68397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 21287 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) : 1.828798 object centre at (A) : 24.03750 7.039001 83.32401 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1681338E-02 4.5796218E-03 midg,1,midg; midg,igrid,midg 0.1584068 0.1531353 1,midg,midg; igrid,midg,midg 0.6155711 -0.1801037 gauss-seidel spectral radius is 0.9992300 estimated iterations to convergence 284 setup time was (sec) 1.960000 now iterating at: 01:13:08 rms-change max change #iterations 9.751806 358.9887 at 10iterations 5.584588 126.6802 at 20iterations 3.185609 69.88911 at 30iterations 1.815549 36.24366 at 40iterations 1.031612 22.67020 at 50iterations 0.5870088 10.64327 at 60iterations 0.3330192 6.343672 at 70iterations 0.1889049 3.569721 at 80iterations 0.1077031 2.008667 at 90iterations 6.1189715E-02 1.126389 at 100iterations 3.4706075E-02 0.6535645 at 110iterations 1.9779311E-02 0.3937891 at 120iterations 1.1358302E-02 0.2197571 at 130iterations 6.5418915E-03 0.1292229 at 140iterations 3.8200032E-03 8.8487625E-02 at 150iterations 2.2804621E-03 5.3066254E-02 at 160iterations 1.4096140E-03 3.2707214E-02 at 170iterations 9.1650122E-04 2.3235321E-02 at 180iterations finished qdiffx linear iterations at : 01:13:22 total time elapsed so far: 15.76000 # loops : 180 mean,max change (kT/e) : 9.1650122E-04 2.3235321E-02 energy calculations done at 15.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 01:13:23 15.938u 0.345s 0:16.59 98.0% 0+0k 0+0io 0pf+0w