Mon Oct 10 16:04:09 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 Mon Oct 10 2011 at 16:04:09 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4322 !!! WARNING: ASP 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5467502 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): -58.93400 -7.433000 ymin,ymax (A): -29.76800 34.26400 zmin,zma (A): -35.97800 29.13400 x,y,z range (A): 51.50100 64.03200 65.11200 scale (grids/A): 0.5467502 object centre (A): -33.18350 2.248000 -3.422001 number of atom coordinates read : 4322 total number of charged atoms : 4223 net assigned charge : 5.500020 assigned positive charge : 656.3632 centred at (gu) : 90.21593 89.68591 91.57410 assigned negative charge : -650.8663 centred at (gu) : 90.26112 89.65569 91.59967 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8484 nv = 96 ne = 84 npr = 86500 no. pairs analyzed = 86500 no. exposed pairs = 5378 no. arc points = 36603 no. surface atoms = 1804 nbur = 2518 mkacc time = 0.1500000 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 = 1.568000 m= 363 mr = 4679 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2900000 number of dielectric boundary points 4156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3757 ## 493 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 11221 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1862597E-10 1.4300769E-10 midg,1,midg; midg,igrid,midg 5.8927391E-11 6.1047911E-10 1,midg,midg; igrid,midg,midg 7.6549111E-10 -1.0132514E-10 gauss-seidel spectral radius is 0.9828537 estimated iterations to convergence 63 setup time was (sec) 0.4800000 now iterating at: 16:04:10 rms-change max change #iterations 9.2428662E-02 13.00726 at 10iterations 6.6124005E-03 0.8874111 at 20iterations 9.5344748E-04 0.1727486 at 30iterations 3.4582507E-04 5.2566528E-02 at 40iterations 1.4737737E-04 2.0206451E-02 at 50iterations finished qdiffx linear iterations at : 16:04:13 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.4737737E-04 2.0206451E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 16:04:14 3.567u 0.191s 0:04.18 89.7% 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 Mon Oct 10 2011 at 16:04:14 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4322 !!! WARNING: ASP 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.640251 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): -58.93400 -7.433000 ymin,ymax (A): -29.76800 34.26400 zmin,zma (A): -35.97800 29.13400 x,y,z range (A): 51.50100 64.03200 65.11200 scale (grids/A): 1.640251 object centre (A): -33.18350 2.248000 -3.422001 number of atom coordinates read : 4322 total number of charged atoms : 4223 net assigned charge : 5.500020 assigned positive charge : 656.3632 centred at (gu) : 90.64649 89.05629 94.72077 assigned negative charge : -650.8663 centred at (gu) : 90.78304 88.96639 94.79877 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 94751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30655 mr = 67014 m= 3322 mr = 21375 m= 106 mr = 1651 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 418 time to turn everything in is 0.4700000 number of dielectric boundary points 38788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 32331 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) : 0.5467502 object centre at (A) : -33.18350 2.248000 -3.422001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7711405E-03 1.4674688E-02 midg,1,midg; midg,igrid,midg 2.0545850E-02 1.7933322E-02 1,midg,midg; igrid,midg,midg 1.7966770E-03 7.1264460E-04 gauss-seidel spectral radius is 0.9983412 estimated iterations to convergence 195 setup time was (sec) 0.7200000 now iterating at: 16:04:15 rms-change max change #iterations 4.175851 181.6672 at 10iterations 1.808330 54.10515 at 20iterations 0.7861669 26.55383 at 30iterations 0.3409558 9.893880 at 40iterations 0.1481416 4.642204 at 50iterations 6.4509556E-02 2.019493 at 60iterations 2.8068202E-02 0.8204803 at 70iterations 1.2278568E-02 0.4060440 at 80iterations 5.3931796E-03 0.1516495 at 90iterations 2.4254865E-03 7.4333191E-02 at 100iterations 1.1399589E-03 4.0400505E-02 at 110iterations 5.9025793E-04 1.8764496E-02 at 120iterations finished qdiffx linear iterations at : 16:04:23 total time elapsed so far: 8.700000 # loops : 120 mean,max change (kT/e) : 5.9025793E-04 1.8764496E-02 energy calculations done at 8.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.830000 DelPhi exited at 16:04:23 8.828u 0.269s 0:09.48 95.7% 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 Mon Oct 10 2011 at 16:04:23 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4322 !!! WARNING: ASP 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.460376 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): -58.93400 -7.433000 ymin,ymax (A): -29.76800 34.26400 zmin,zma (A): -35.97800 29.13400 x,y,z range (A): 51.50100 64.03200 65.11200 scale (grids/A): 2.460376 object centre (A): -33.18350 2.248000 -3.422001 number of atom coordinates read : 4322 total number of charged atoms : 4223 net assigned charge : 5.500020 assigned positive charge : 656.3632 centred at (gu) : 90.96943 88.58414 97.08088 assigned negative charge : -650.8663 centred at (gu) : 91.17432 88.44942 97.19804 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 220454 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105620 mr = 163684 m= 30873 mr = 84216 m= 5166 mr = 23325 m= 439 mr = 3408 m= 4 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1364 time to turn everything in is 1.160000 number of dielectric boundary points 87759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 33753 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) : 1.640251 object centre at (A) : -33.18350 2.248000 -3.422001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9452833E-02 0.5343831 midg,1,midg; midg,igrid,midg 0.4227741 0.2471708 1,midg,midg; igrid,midg,midg 4.3343697E-02 2.4533380E-02 gauss-seidel spectral radius is 0.9992219 estimated iterations to convergence 283 setup time was (sec) 1.460000 now iterating at: 16:04:25 rms-change max change #iterations 10.86208 328.0243 at 10iterations 6.342365 141.0266 at 20iterations 3.691639 77.61118 at 30iterations 2.137282 44.05320 at 40iterations 1.232141 25.45366 at 50iterations 0.7080429 13.60868 at 60iterations 0.4060652 7.191486 at 70iterations 0.2323067 3.968409 at 80iterations 0.1327669 2.273766 at 90iterations 7.5842455E-02 1.399532 at 100iterations 4.3272685E-02 0.7273216 at 110iterations 2.4673697E-02 0.4346943 at 120iterations 1.4053232E-02 0.2516708 at 130iterations 8.0196774E-03 0.1496487 at 140iterations 4.5914133E-03 7.8372955E-02 at 150iterations 2.6374406E-03 4.8511505E-02 at 160iterations 1.5296979E-03 2.6170731E-02 at 170iterations 9.0682931E-04 1.7642975E-02 at 180iterations finished qdiffx linear iterations at : 16:04:37 total time elapsed so far: 13.48000 # loops : 180 mean,max change (kT/e) : 9.0682931E-04 1.7642975E-02 energy calculations done at 13.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.62000 DelPhi exited at 16:04:37 13.623u 0.297s 0:14.23 97.7% 0+0k 0+0io 0pf+0w