Sat Oct 15 11:40:21 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 11:40:21 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6431333 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): 5.783000 61.13700 ymin,ymax (A): 2.910000 50.13400 zmin,zma (A): 14.67000 55.90400 x,y,z range (A): 55.35400 47.22400 41.23400 scale (grids/A): 0.6431333 object centre (A): 33.46000 26.52200 35.28700 number of atom coordinates read : 2042 total number of charged atoms : 1902 net assigned charge : 0.9200045 assigned positive charge : 306.8247 centred at (gu) : 87.25333 89.45427 89.18448 assigned negative charge : -305.9049 centred at (gu) : 87.40477 89.48298 89.18256 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5669 nv = 96 ne = 84 npr = 41076 no. pairs analyzed = 41076 no. exposed pairs = 2594 no. arc points = 18498 no. surface atoms = 877 nbur = 1165 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 3047 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1666 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6590 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3297825E-10 9.9688835E-10 midg,1,midg; midg,igrid,midg 4.2976946E-09 -1.6559458E-09 1,midg,midg; igrid,midg,midg 2.8841885E-08 -7.9173201E-09 gauss-seidel spectral radius is 0.9874246 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 11:40:23 rms-change max change #iterations 0.1316809 21.89866 at 10iterations 1.3209857E-02 2.560593 at 20iterations 1.3457460E-03 0.1995335 at 30iterations 1.3557133E-04 2.1520615E-02 at 40iterations 1.5320324E-05 2.5901794E-03 at 50iterations finished qdiffx linear iterations at : 11:40:29 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 1.5320324E-05 2.5901794E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 11:40:30 4.153u 0.332s 0:09.67 46.3% 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 11:40:32 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.929400 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): 5.783000 61.13700 ymin,ymax (A): 2.910000 50.13400 zmin,zma (A): 14.67000 55.90400 x,y,z range (A): 55.35400 47.22400 41.23400 scale (grids/A): 1.929400 object centre (A): 33.46000 26.52200 35.28700 number of atom coordinates read : 2042 total number of charged atoms : 1902 net assigned charge : 0.9200045 assigned positive charge : 306.8247 centred at (gu) : 81.76006 88.36276 87.55347 assigned negative charge : -305.9049 centred at (gu) : 82.21427 88.44875 87.54752 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 61230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18498 grid for indexing accessible points = 1.400000 m= 21521 mr = 41790 m= 3244 mr = 15370 m= 180 mr = 1919 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.5800000 number of dielectric boundary points 27071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14976 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) : 0.6431333 object centre at (A) : 33.46000 26.52200 35.28700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1340065E-03 1.5008914E-03 midg,1,midg; midg,igrid,midg 2.4524651E-02 9.5297146E-04 1,midg,midg; igrid,midg,midg -3.2407191E-02 -4.2378131E-02 gauss-seidel spectral radius is 0.9986095 estimated iterations to convergence 213 setup time was (sec) 0.8800000 now iterating at: 11:40:37 rms-change max change #iterations 3.848922 178.1215 at 10iterations 1.782939 61.55790 at 20iterations 0.8342475 29.22894 at 30iterations 0.3864824 13.29691 at 40iterations 0.1798521 6.060491 at 50iterations 8.3733395E-02 2.982358 at 60iterations 3.8803849E-02 1.449860 at 70iterations 1.8084576E-02 0.6209960 at 80iterations 8.4276982E-03 0.2946625 at 90iterations 3.9204974E-03 0.1323280 at 100iterations 1.8202270E-03 6.1092496E-02 at 110iterations 8.4940111E-04 3.0336380E-02 at 120iterations finished qdiffx linear iterations at : 11:40:58 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 8.4940111E-04 3.0336380E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 11:40:59 9.607u 0.319s 0:26.82 36.9% 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 15 2011 at 11:40:59 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.894100 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): 5.783000 61.13700 ymin,ymax (A): 2.910000 50.13400 zmin,zma (A): 14.67000 55.90400 x,y,z range (A): 55.35400 47.22400 41.23400 scale (grids/A): 2.894100 object centre (A): 33.46000 26.52200 35.28700 number of atom coordinates read : 2042 total number of charged atoms : 1902 net assigned charge : 0.9200045 assigned positive charge : 306.8247 centred at (gu) : 77.64005 87.54404 86.33008 assigned negative charge : -305.9049 centred at (gu) : 78.32127 87.67310 86.32128 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 141698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18498 grid for indexing accessible points = 1.400000 m= 69938 mr = 101592 m= 24467 mr = 56295 m= 5788 mr = 19217 m= 784 mr = 4104 m= 26 mr = 458 m= 0 mr = 4 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 1072 time to turn everything in is 1.440000 number of dielectric boundary points 61031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 15212 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) : 1.929400 object centre at (A) : 33.46000 26.52200 35.28700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4771088E-02 5.1723127E-03 midg,1,midg; midg,igrid,midg 0.2709223 -5.2560095E-02 1,midg,midg; igrid,midg,midg -0.6473275 -0.7228658 gauss-seidel spectral radius is 0.9992417 estimated iterations to convergence 287 setup time was (sec) 1.780000 now iterating at: 11:41:06 rms-change max change #iterations 9.073264 376.1686 at 10iterations 5.277317 125.2220 at 20iterations 3.051598 68.56190 at 30iterations 1.766044 37.40626 at 40iterations 1.016438 24.21337 at 50iterations 0.5837676 11.85359 at 60iterations 0.3347219 7.092392 at 70iterations 0.1920720 3.920921 at 80iterations 0.1098408 2.226241 at 90iterations 6.2998213E-02 1.309814 at 100iterations 3.5993550E-02 0.6913624 at 110iterations 2.0537818E-02 0.4725037 at 120iterations 1.1743939E-02 0.2474060 at 130iterations 6.7079575E-03 0.1278110 at 140iterations 3.8360255E-03 7.6118469E-02 at 150iterations 2.1944209E-03 4.2581558E-02 at 160iterations 1.2563893E-03 2.3906708E-02 at 170iterations 7.2076445E-04 1.3862610E-02 at 180iterations finished qdiffx linear iterations at : 11:41:37 total time elapsed so far: 15.67000 # loops : 180 mean,max change (kT/e) : 7.2076445E-04 1.3862610E-02 energy calculations done at 15.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.85000 DelPhi exited at 11:41:38 15.850u 0.359s 0:39.03 41.5% 0+0k 0+0io 0pf+0w