Sun Oct 9 18:35:56 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+sph.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 = amb.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 Sun Oct 9 2011 at 18:35:56 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5248 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5377969 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): 3.330000 68.29300 ymin,ymax (A): -8.983000 56.81200 zmin,zma (A): -2.666000 63.53000 x,y,z range (A): 64.96300 65.79500 66.19600 scale (grids/A): 0.5377969 object centre (A): 35.81150 23.91450 30.43200 number of atom coordinates read : 5248 total number of charged atoms : 5114 net assigned charge : 3.621048 assigned positive charge : 807.7361 centred at (gu) : 88.20447 88.49728 89.48814 assigned negative charge : -804.1216 centred at (gu) : 88.08102 88.53909 89.42842 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9905 nv = 96 ne = 84 npr = 105163 no. pairs analyzed = 105163 no. exposed pairs = 6200 no. arc points = 42499 no. surface atoms = 2119 nbur = 3129 mkacc time = 0.3000000 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 = 1.596000 m= 429 mr = 5580 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 4729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4282 ## 464 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 13053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9452830E-10 6.1471300E-10 midg,1,midg; midg,igrid,midg 7.9786422E-10 -1.2549561E-10 1,midg,midg; igrid,midg,midg -1.4610370E-09 7.9254492E-10 gauss-seidel spectral radius is 0.9823442 estimated iterations to convergence 62 setup time was (sec) 0.8600000 now iterating at: 18:35:57 rms-change max change #iterations 9.5300116E-02 15.49989 at 10iterations 8.7150726E-03 1.206547 at 20iterations 2.5571578E-03 0.2863426 at 30iterations 1.1282978E-03 0.1356701 at 40iterations 5.1324407E-04 6.6300154E-02 at 50iterations finished qdiffx linear iterations at : 18:36:00 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 5.1324407E-04 6.6300154E-02 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 18:36:01 4.334u 0.265s 0:04.89 93.8% 0+0k 0+0io 6pf+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 Sun Oct 9 2011 at 18:36:01 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5248 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.613391 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): 3.330000 68.29300 ymin,ymax (A): -8.983000 56.81200 zmin,zma (A): -2.666000 63.53000 x,y,z range (A): 64.96300 65.79500 66.19600 scale (grids/A): 1.613391 object centre (A): 35.81150 23.91450 30.43200 number of atom coordinates read : 5248 total number of charged atoms : 5114 net assigned charge : 3.621048 assigned positive charge : 807.7361 centred at (gu) : 84.61175 85.49065 88.46288 assigned negative charge : -804.1216 centred at (gu) : 84.24303 85.61723 88.28501 start vw surface at 0.2200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 111327 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 37418 mr = 80291 m= 4112 mr = 26533 m= 111 mr = 2044 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 44099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 476 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 39038 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) : 0.5377969 object centre at (A) : 35.81150 23.91450 30.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9456590E-02 -6.2213903E-03 midg,1,midg; midg,igrid,midg 2.4597669E-02 2.5710264E-02 1,midg,midg; igrid,midg,midg -4.9701463E-03 1.3909079E-02 gauss-seidel spectral radius is 0.9983485 estimated iterations to convergence 195 setup time was (sec) 1.270000 now iterating at: 18:36:02 rms-change max change #iterations 4.591141 158.8356 at 10iterations 1.992982 59.67209 at 20iterations 0.8666014 27.07681 at 30iterations 0.3767241 11.80400 at 40iterations 0.1644813 5.010189 at 50iterations 7.2260305E-02 1.989055 at 60iterations 3.2062709E-02 0.8816833 at 70iterations 1.4692969E-02 0.4381599 at 80iterations 7.3048607E-03 0.2095566 at 90iterations 4.1153901E-03 0.1155319 at 100iterations 2.6575723E-03 7.6915741E-02 at 110iterations 1.8754252E-03 5.1580429E-02 at 120iterations finished qdiffx linear iterations at : 18:36:11 total time elapsed so far: 9.770000 # loops : 120 mean,max change (kT/e) : 1.8754252E-03 5.1580429E-02 energy calculations done at 9.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.950000 DelPhi exited at 18:36:11 9.956u 0.304s 0:10.53 97.3% 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 Sun Oct 9 2011 at 18:36:11 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5248 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.420086 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): 3.330000 68.29300 ymin,ymax (A): -8.983000 56.81200 zmin,zma (A): -2.666000 63.53000 x,y,z range (A): 64.96300 65.79500 66.19600 scale (grids/A): 2.420086 object centre (A): 35.81150 23.91450 30.43200 number of atom coordinates read : 5248 total number of charged atoms : 5114 net assigned charge : 3.621048 assigned positive charge : 807.7361 centred at (gu) : 81.91716 83.23550 87.69392 assigned negative charge : -804.1216 centred at (gu) : 81.36442 83.42568 87.42760 start vw surface at 0.2200000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 258623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 128065 mr = 195408 m= 38704 mr = 103606 m= 6552 mr = 29577 m= 439 mr = 4245 m= 6 mr = 152 m= 0 mr = 0 time to grow re-entrant surface = 1.540000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.450000 number of dielectric boundary points 99401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 2.610000 number of grid points assigned charge 40862 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) : 1.613391 object centre at (A) : 35.81150 23.91450 30.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2859064 -0.2229702 midg,1,midg; midg,igrid,midg 0.2241067 0.5847291 1,midg,midg; igrid,midg,midg -0.1328392 0.1635961 gauss-seidel spectral radius is 0.9992321 estimated iterations to convergence 285 setup time was (sec) 2.780000 now iterating at: 18:36:14 rms-change max change #iterations 11.88714 303.4579 at 10iterations 6.970254 132.2235 at 20iterations 4.052159 80.46062 at 30iterations 2.345383 53.89868 at 40iterations 1.352482 26.66131 at 50iterations 0.7770244 15.22074 at 60iterations 0.4467214 7.586092 at 70iterations 0.2557136 4.373947 at 80iterations 0.1462869 2.344754 at 90iterations 8.4010758E-02 1.456790 at 100iterations 4.8110399E-02 0.7560272 at 110iterations 2.7657032E-02 0.4514604 at 120iterations 1.6093476E-02 0.2943740 at 130iterations 9.5102591E-03 0.1774788 at 140iterations 5.8042007E-03 0.1065063 at 150iterations 3.7476264E-03 6.7269325E-02 at 160iterations 2.5980349E-03 4.7065735E-02 at 170iterations 1.9249958E-03 3.5551071E-02 at 180iterations finished qdiffx linear iterations at : 18:36:29 total time elapsed so far: 17.17000 # loops : 180 mean,max change (kT/e) : 1.9249958E-03 3.5551071E-02 energy calculations done at 17.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.34000 DelPhi exited at 18:36:29 17.344u 0.322s 0:17.93 98.4% 0+0k 0+0io 0pf+0w