Sun Oct 9 14:53:55 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 14:53:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1245 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 214 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7284185 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): 42.99700 91.87000 ymin,ymax (A): -27.94300 14.91700 zmin,zma (A): -31.71700 16.42900 x,y,z range (A): 48.87300 42.86000 48.14600 scale (grids/A): 0.7284185 object centre (A): 67.43350 -6.513000 -7.643999 number of atom coordinates read : 1245 total number of charged atoms : 1115 net assigned charge : 1.500005 assigned positive charge : 178.6483 centred at (gu) : 89.61139 89.84604 92.19596 assigned negative charge : -177.1481 centred at (gu) : 89.60609 89.66160 92.10002 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4756 nv = 96 ne = 84 npr = 24425 no. pairs analyzed = 24425 no. exposed pairs = 1702 no. arc points = 12676 no. surface atoms = 570 nbur = 675 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 279 mr = 2419 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.1300000 number of dielectric boundary points 2566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1000 ## 95 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4725 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4751754E-08 9.3975629E-08 midg,1,midg; midg,igrid,midg -6.5041391E-08 9.6497338E-08 1,midg,midg; igrid,midg,midg 1.8536140E-08 2.0439655E-08 gauss-seidel spectral radius is 0.9901009 estimated iterations to convergence 82 setup time was (sec) 0.3100000 now iterating at: 14:53:55 rms-change max change #iterations 0.1754207 35.45292 at 10iterations 2.2819581E-02 3.753795 at 20iterations 2.8351094E-03 0.4547958 at 30iterations 3.6580247E-04 6.6521645E-02 at 40iterations 4.6896974E-05 7.4243546E-03 at 50iterations finished qdiffx linear iterations at : 14:53:58 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.6896974E-05 7.4243546E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:53:58 3.320u 0.167s 0:03.80 91.5% 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 14:53:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1245 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 214 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.185256 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): 42.99700 91.87000 ymin,ymax (A): -27.94300 14.91700 zmin,zma (A): -31.71700 16.42900 x,y,z range (A): 48.87300 42.86000 48.14600 scale (grids/A): 2.185256 object centre (A): 67.43350 -6.513000 -7.643999 number of atom coordinates read : 1245 total number of charged atoms : 1115 net assigned charge : 1.500005 assigned positive charge : 178.6483 centred at (gu) : 88.83452 89.53838 96.58813 assigned negative charge : -177.1481 centred at (gu) : 88.81834 88.98502 96.30013 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 49225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12676 grid for indexing accessible points = 1.400000 m= 18648 mr = 31539 m= 3760 mr = 13872 m= 286 mr = 2590 m= 2 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 3216 time to turn everything in is 0.2700000 number of dielectric boundary points 23787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8877 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) : 0.7284185 object centre at (A) : 67.43350 -6.513000 -7.643999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0801419E-03 1.2379724E-02 midg,1,midg; midg,igrid,midg -1.0756423E-03 2.9293863E-02 1,midg,midg; igrid,midg,midg 1.5028960E-02 1.6939979E-02 gauss-seidel spectral radius is 0.9988196 estimated iterations to convergence 230 setup time was (sec) 0.4800000 now iterating at: 14:53:59 rms-change max change #iterations 3.607299 175.3248 at 10iterations 1.770317 70.13751 at 20iterations 0.8685666 34.72614 at 30iterations 0.4280465 16.66829 at 40iterations 0.2100604 7.847861 at 50iterations 0.1038182 4.044178 at 60iterations 5.1024444E-02 1.829966 at 70iterations 2.5024185E-02 1.072328 at 80iterations 1.2355395E-02 0.4671135 at 90iterations 6.1028069E-03 0.2461853 at 100iterations 3.0021879E-03 0.1127510 at 110iterations 1.4835089E-03 5.4031372E-02 at 120iterations finished qdiffx linear iterations at : 14:54:06 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.4835089E-03 5.4031372E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 14:54:07 7.603u 0.187s 0:08.10 96.0% 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 14:54:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1245 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 214 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.277883 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): 42.99700 91.87000 ymin,ymax (A): -27.94300 14.91700 zmin,zma (A): -31.71700 16.42900 x,y,z range (A): 48.87300 42.86000 48.14600 scale (grids/A): 3.277883 object centre (A): 67.43350 -6.513000 -7.643999 number of atom coordinates read : 1245 total number of charged atoms : 1115 net assigned charge : 1.500005 assigned positive charge : 178.6483 centred at (gu) : 88.25178 89.30758 99.88217 assigned negative charge : -177.1481 centred at (gu) : 88.22754 88.47750 99.45023 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 113096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12676 grid for indexing accessible points = 1.400000 m= 57541 mr = 76448 m= 23788 mr = 46835 m= 7183 mr = 19470 m= 1201 mr = 5670 m= 98 mr = 813 m= 4 mr = 72 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 10612 time to turn everything in is 0.7800000 number of dielectric boundary points 53601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 8916 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) : 2.185256 object centre at (A) : 67.43350 -6.513000 -7.643999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5309856E-02 0.4016292 midg,1,midg; midg,igrid,midg -2.5402920E-02 0.2091172 1,midg,midg; igrid,midg,midg 0.1886012 0.1838493 gauss-seidel spectral radius is 0.9993028 estimated iterations to convergence 299 setup time was (sec) 1.010000 now iterating at: 14:54:08 rms-change max change #iterations 8.066834 709.6412 at 10iterations 4.771950 118.0547 at 20iterations 2.818059 69.72491 at 30iterations 1.653222 39.30545 at 40iterations 0.9681150 22.63145 at 50iterations 0.5681328 13.37222 at 60iterations 0.3328075 7.504699 at 70iterations 0.1943938 4.929304 at 80iterations 0.1138156 2.754323 at 90iterations 6.6267848E-02 1.435798 at 100iterations 3.8738508E-02 0.7565560 at 110iterations 2.2548074E-02 0.4599380 at 120iterations 1.3200902E-02 0.2776177 at 130iterations 7.6886821E-03 0.1712294 at 140iterations 4.4743731E-03 9.0759277E-02 at 150iterations 2.6118532E-03 5.4855585E-02 at 160iterations 1.5245066E-03 3.0313492E-02 at 170iterations 8.9025620E-04 1.8392563E-02 at 180iterations finished qdiffx linear iterations at : 14:54:19 total time elapsed so far: 11.98000 # loops : 180 mean,max change (kT/e) : 8.9025620E-04 1.8392563E-02 energy calculations done at 11.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 14:54:19 12.120u 0.197s 0:12.64 97.3% 0+0k 0+0io 0pf+0w