Wed Dec 28 11:01:55 PST 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 Wed Dec 28 2011 at 11:01:55 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 0.6336662 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): -35.09600 10.37300 ymin,ymax (A): 1.525000 41.70100 zmin,zma (A): 8.0999970E-02 56.26200 x,y,z range (A): 45.46900 40.17600 56.18100 scale (grids/A): 0.6336662 object centre (A): -12.36150 21.61300 28.17150 number of atom coordinates read : 1968 total number of charged atoms : 1768 net assigned charge : -21.95202 assigned positive charge : 266.7204 centred at (gu) : 90.29427 89.35334 89.82436 assigned negative charge : -288.6722 centred at (gu) : 90.19527 89.50452 89.82950 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5345 nv = 96 ne = 84 npr = 40613 no. pairs analyzed = 40613 no. exposed pairs = 2404 no. arc points = 16832 no. surface atoms = 821 nbur = 1147 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3047 m= 1 mr = 40 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 0.2900000 number of dielectric boundary points 2579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1555 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6194 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7291373E-08 -2.6086942E-08 midg,1,midg; midg,igrid,midg -1.8043950E-08 -3.3056338E-08 1,midg,midg; igrid,midg,midg -3.1939756E-08 -2.0756678E-08 gauss-seidel spectral radius is 0.9870427 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 11:01:56 rms-change max change #iterations 0.1275115 22.14723 at 10iterations 1.2291878E-02 2.348091 at 20iterations 1.2125783E-03 0.2100677 at 30iterations 1.1554160E-04 1.7883301E-02 at 40iterations 1.1293640E-05 1.6174316E-03 at 50iterations finished qdiffx linear iterations at : 11:02:00 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 1.1293640E-05 1.6174316E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 11:02:01 4.673u 0.505s 0:06.38 81.0% 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 Wed Dec 28 2011 at 11:02:01 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 1.900999 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): -35.09600 10.37300 ymin,ymax (A): 1.525000 41.70100 zmin,zma (A): 8.0999970E-02 56.26200 x,y,z range (A): 45.46900 40.17600 56.18100 scale (grids/A): 1.900999 object centre (A): -12.36150 21.61300 28.17150 number of atom coordinates read : 1968 total number of charged atoms : 1768 net assigned charge : -21.95202 assigned positive charge : 266.7204 centred at (gu) : 90.88316 88.06023 89.47334 assigned negative charge : -288.6722 centred at (gu) : 90.58620 88.51360 89.48862 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 21925 mr = 40258 m= 3631 mr = 16803 m= 202 mr = 2409 m= 2 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 23943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 13915 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) : 0.6336662 object centre at (A) : -12.36150 21.61300 28.17150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0135428E-02 -6.0402803E-02 midg,1,midg; midg,igrid,midg -3.1528175E-02 -4.0870920E-02 1,midg,midg; igrid,midg,midg -2.7536690E-02 -3.7896365E-02 gauss-seidel spectral radius is 0.9985551 estimated iterations to convergence 209 setup time was (sec) 0.9400000 now iterating at: 11:02:03 rms-change max change #iterations 3.563706 163.9372 at 10iterations 1.629946 60.63638 at 20iterations 0.7495711 30.01733 at 30iterations 0.3437565 13.16762 at 40iterations 0.1575350 6.120769 at 50iterations 7.2156087E-02 2.529101 at 60iterations 3.3155352E-02 1.074158 at 70iterations 1.5062654E-02 0.5793552 at 80iterations 6.9299112E-03 0.2439651 at 90iterations 3.1737725E-03 0.1094818 at 100iterations 1.4584055E-03 5.0627347E-02 at 110iterations 6.6848489E-04 2.2941589E-02 at 120iterations finished qdiffx linear iterations at : 11:02:13 total time elapsed so far: 11.17000 # loops : 120 mean,max change (kT/e) : 6.6848489E-04 2.2941589E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 11:02:14 11.355u 0.519s 0:13.00 91.2% 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 Wed Dec 28 2011 at 11:02:15 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.851498 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): -35.09600 10.37300 ymin,ymax (A): 1.525000 41.70100 zmin,zma (A): 8.0999970E-02 56.26200 x,y,z range (A): 45.46900 40.17600 56.18100 scale (grids/A): 2.851498 object centre (A): -12.36150 21.61300 28.17150 number of atom coordinates read : 1968 total number of charged atoms : 1768 net assigned charge : -21.95202 assigned positive charge : 266.7204 centred at (gu) : 91.32489 87.09048 89.20998 assigned negative charge : -288.6722 centred at (gu) : 90.87944 87.77052 89.23307 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 133101 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 70021 mr = 96870 m= 26559 mr = 58582 m= 6540 mr = 21996 m= 896 mr = 5117 m= 39 mr = 613 m= 0 mr = 18 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 53960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 14140 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) : 1.900999 object centre at (A) : -12.36150 21.61300 28.17150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7832291 -0.9070751 midg,1,midg; midg,igrid,midg -0.3439111 -0.4324848 1,midg,midg; igrid,midg,midg -0.2863187 -0.3955353 gauss-seidel spectral radius is 0.9992197 estimated iterations to convergence 283 setup time was (sec) 1.840000 now iterating at: 11:02:18 rms-change max change #iterations 8.279494 356.3988 at 10iterations 4.718178 113.7986 at 20iterations 2.664589 58.06747 at 30iterations 1.513218 29.16345 at 40iterations 0.8511428 16.58055 at 50iterations 0.4830875 10.77805 at 60iterations 0.2722447 6.316161 at 70iterations 0.1540425 3.142232 at 80iterations 8.7118901E-02 1.868120 at 90iterations 4.9326383E-02 0.9932556 at 100iterations 2.7872879E-02 0.5317345 at 110iterations 1.5750818E-02 0.3245802 at 120iterations 8.8879047E-03 0.1714973 at 130iterations 5.0240788E-03 0.1088333 at 140iterations 2.8406926E-03 5.4704666E-02 at 150iterations 1.6067082E-03 3.3081055E-02 at 160iterations 9.1133692E-04 1.9617081E-02 at 170iterations 5.1521143E-04 1.0475159E-02 at 180iterations finished qdiffx linear iterations at : 11:02:35 total time elapsed so far: 19.20000 # loops : 180 mean,max change (kT/e) : 5.1521143E-04 1.0475159E-02 energy calculations done at 19.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.39000 DelPhi exited at 11:02:36 19.388u 0.514s 0:21.24 93.6% 0+0k 0+0io 0pf+0w