Sat Oct 8 11:42:06 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 11:42:06 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5354 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 470 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.5265415 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): 7.364000 72.39600 ymin,ymax (A): 1.247000 68.85800 zmin,zma (A): 9.486000 75.36300 x,y,z range (A): 65.03200 67.61100 65.87700 scale (grids/A): 0.5265415 object centre (A): 39.88000 35.05250 42.42450 number of atom coordinates read : 5354 total number of charged atoms : 5180 net assigned charge : 0.4480405 assigned positive charge : 815.0725 centred at (gu) : 90.35640 90.89120 91.20966 assigned negative charge : -814.6302 centred at (gu) : 90.29598 90.87743 91.25082 start vw surface at 0.2700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 9140 nv = 96 ne = 84 npr = 111268 no. pairs analyzed = 111268 no. exposed pairs = 6314 no. arc points = 42971 no. surface atoms = 2123 nbur = 3231 mkacc time = 0.3200000 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 = 1.624000 m= 328 mr = 4974 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 4486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4249 ## 553 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 12331 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8137962E-10 -3.0633079E-10 midg,1,midg; midg,igrid,midg -5.1601851E-11 1.1630445E-10 1,midg,midg; igrid,midg,midg -3.0478958E-10 3.9102679E-10 gauss-seidel spectral radius is 0.9815796 estimated iterations to convergence 61 setup time was (sec) 0.9200000 now iterating at: 11:42:07 rms-change max change #iterations 8.5894719E-02 11.49366 at 10iterations 6.7488132E-03 1.331947 at 20iterations 1.1645452E-03 0.2957764 at 30iterations 2.9683349E-04 7.1601868E-02 at 40iterations 8.2525497E-05 1.7829895E-02 at 50iterations finished qdiffx linear iterations at : 11:42:10 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 8.2525497E-05 1.7829895E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 11:42:10 4.366u 0.189s 0:04.83 93.9% 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 Sat Oct 8 2011 at 11:42:11 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5354 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 470 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.579625 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): 7.364000 72.39600 ymin,ymax (A): 1.247000 68.85800 zmin,zma (A): 9.486000 75.36300 x,y,z range (A): 65.03200 67.61100 65.87700 scale (grids/A): 1.579625 object centre (A): 39.88000 35.05250 42.42450 number of atom coordinates read : 5354 total number of charged atoms : 5180 net assigned charge : 0.4480405 assigned positive charge : 815.0725 centred at (gu) : 91.06745 92.67204 93.62751 assigned negative charge : -814.6302 centred at (gu) : 90.88744 92.63195 93.75230 start vw surface at 0.2800000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 103309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42971 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 30796 mr = 72740 m= 2888 mr = 21119 m= 57 mr = 1306 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1081 time to turn everything in is 0.9800000 number of dielectric boundary points 41882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 507 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 39279 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) : 0.5265415 object centre at (A) : 39.88000 35.05250 42.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3100130E-02 -3.4742120E-03 midg,1,midg; midg,igrid,midg 1.0255973E-03 1.7454486E-02 1,midg,midg; igrid,midg,midg -1.0953953E-02 9.1190552E-03 gauss-seidel spectral radius is 0.9982771 estimated iterations to convergence 191 setup time was (sec) 1.330000 now iterating at: 11:42:12 rms-change max change #iterations 4.384367 168.8360 at 10iterations 1.863768 56.80048 at 20iterations 0.7950264 23.00880 at 30iterations 0.3400223 10.46642 at 40iterations 0.1451073 4.690996 at 50iterations 6.2430393E-02 1.886805 at 60iterations 2.6915401E-02 0.7620125 at 70iterations 1.1664279E-02 0.3328857 at 80iterations 5.0962437E-03 0.1696548 at 90iterations 2.2928582E-03 8.1138611E-02 at 100iterations 1.0749999E-03 4.0145874E-02 at 110iterations 5.3653336E-04 2.3620605E-02 at 120iterations finished qdiffx linear iterations at : 11:42:21 total time elapsed so far: 10.32000 # loops : 120 mean,max change (kT/e) : 5.3653336E-04 2.3620605E-02 energy calculations done at 10.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.55000 DelPhi exited at 11:42:22 10.554u 0.250s 0:11.14 96.9% 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 Sat Oct 8 2011 at 11:42:22 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5354 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 470 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.369437 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): 7.364000 72.39600 ymin,ymax (A): 1.247000 68.85800 zmin,zma (A): 9.486000 75.36300 x,y,z range (A): 65.03200 67.61100 65.87700 scale (grids/A): 2.369437 object centre (A): 39.88000 35.05250 42.42450 number of atom coordinates read : 5354 total number of charged atoms : 5180 net assigned charge : 0.4480405 assigned positive charge : 815.0725 centred at (gu) : 91.60078 94.00745 95.44089 assigned negative charge : -814.6302 centred at (gu) : 91.33109 93.94789 95.62835 start vw surface at 0.2700000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 241314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42971 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 108797 mr = 179073 m= 29504 mr = 85695 m= 4248 mr = 21916 m= 250 mr = 2721 m= 2 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 3433 time to turn everything in is 2.270000 number of dielectric boundary points 94618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 2.440000 number of grid points assigned charge 41370 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) : 1.579625 object centre at (A) : 39.88000 35.05250 42.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2160385 -0.2411315 midg,1,midg; midg,igrid,midg 4.3457825E-02 0.1758921 1,midg,midg; igrid,midg,midg -0.2132172 5.5114508E-02 gauss-seidel spectral radius is 0.9992176 estimated iterations to convergence 282 setup time was (sec) 2.650000 now iterating at: 11:42:25 rms-change max change #iterations 11.67198 337.0280 at 10iterations 6.864709 163.0187 at 20iterations 4.019321 96.86646 at 30iterations 2.339717 61.33397 at 40iterations 1.353947 27.81160 at 50iterations 0.7822641 15.34431 at 60iterations 0.4502600 9.218365 at 70iterations 0.2584630 5.509798 at 80iterations 0.1485416 3.067333 at 90iterations 8.5024841E-02 1.645947 at 100iterations 4.8623160E-02 0.8967514 at 110iterations 2.7842015E-02 0.5783157 at 120iterations 1.5923921E-02 0.2883606 at 130iterations 9.1231605E-03 0.1710682 at 140iterations 5.2253827E-03 0.1072350 at 150iterations 3.0124758E-03 5.0709724E-02 at 160iterations 1.7416303E-03 3.0879259E-02 at 170iterations 1.0227712E-03 1.9258499E-02 at 180iterations finished qdiffx linear iterations at : 11:42:38 total time elapsed so far: 15.85000 # loops : 180 mean,max change (kT/e) : 1.0227712E-03 1.9258499E-02 energy calculations done at 15.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.09000 DelPhi exited at 11:42:38 16.093u 0.267s 0:16.63 98.3% 0+0k 0+0io 0pf+0w