solvate a molecule

From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Tue Sep 23 2008 - 00:01:16 CDT

dear friends,
firstly i understand this post should better go to vmd mail list and not here. but as i am not getting any reply there i thought it might be better to ask for help here.

 i have managed to create a non-std molecule (acridine orange) . now the
problem is when i am trying th 'solvate' it in water using vmd(Tk
console) with the command
 % package require solvate
 % solvate aoq.psf aoq.pdb -t 30 -o aoq_wb
the vmd is crashing without giving any error /log. hence i am
not getting any clue about what is going wrong.plz help. i am using Intel/Linux machine
my pdb file is:
REMARK original generated coordinate pdb file
ATOM 1 C MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 2 OT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U O
ATOM 3 OT2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U O
ATOM 4 N MAC 0 0.123 -0.642 0.571 1.00 0.00 U N
ATOM 5 HT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 6 HT2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 7 HT3 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 8 CA MAC 0 -5.107 1.352 1.005 1.00 0.00 U C
ATOM 9 HA MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 10 N2 MAC 0 -4.299 0.713 1.207 1.00 0.00 U N
ATOM 11 HA1 MAC 0 -5.986 1.045 1.614 1.00 0.00 U H
ATOM 12 HA2 MAC 0 -4.830 2.397 1.270 1.00 0.00 U H
ATOM 13 HA3 MAC 0 -5.354 1.307 -0.080 1.00 0.00 U H
ATOM 14 CB MAC 0 -4.392 -0.073 1.897 1.00 0.00 U C
ATOM 15 HB1 MAC 0 -3.663 0.071 2.725 1.00 0.00 U H
ATOM 16 HB2 MAC 0 -5.425 -0.085 2.310 1.00 0.00 U H
ATOM 17 HB3 MAC 0 -4.187 -1.041 1.386 1.00 0.00 U H
ATOM 18 CD1 MAC 0 -3.039 1.934 -0.283 1.00 0.00 U C
ATOM 19 HD1 MAC 0 -3.879 2.612 -0.492 1.00 0.00 U H
ATOM 20 CE1 MAC 0 -1.812 2.120 -0.917 1.00 0.00 U C
ATOM 21 HE1 MAC 0 -1.685 2..949 -1.629 1.00 0.00 U H
ATOM 22 CZ MAC 0 -0.733 1.261 -0.643 1.00 0.00 U C
ATOM 23 CG MAC 0 -3.189 0.892 0.625 1.00 0.00 U C
ATOM 24 CD2 MAC 0 -2.112 0.042 0.894 1.00 0.00 U C
ATOM 25 HD2 MAC 0 -2.248 -0.784 1.607 1.00 0.00 U H
ATOM 26 CE2 MAC 0 -0.879 0.204 0.276 1.00 0.00 U C
ATOM 27 C1 MAC 0 0.512 1.419 -1.262 1.00 0.00 U C
ATOM 28 H1 MAC 0 0.669 2.239 -1.978 1.00 0.00 U H
ATOM 29 C2 MAC 0 1.562 0.544 -0.962 1.00 0.00 U C
ATOM 30 C3 MAC 0 1.315 -0.482 -0.029 1.00 0..00 U C
ATOM 31 C4 MAC 0 2.827 0.670 -1.563 1..00 0.00 U C
ATOM 32 H4 MAC 0 3.013 1.474 -2.290 1.00 0.00 U H
ATOM 33 C5 MAC 0 3.854 -0.212 -1.232 1.00 0.00 U C
ATOM 34 H5 MAC 0 4.846 -0.106 -1.696 1.00 0.00 U H
ATOM 35 C7 MAC 0 2.353 -1.354 0.273 1.00 0.00 U C
ATOM 36 H7 MAC 0 2.175 -2.167 0.992 1.00 0.00 U H
ATOM 37 C6 MAC 0 3.613 -1.234 -0.321 1.00 0.00 U C
ATOM 38 N1 MAC 0 4.671 -2.189 0.006 1.00 0.00 U N
ATOM 39 C8 MAC 0 5.628 -2.116 -0.419 1.00 0.00 U C
ATOM 40 C9 MAC 0 4.407 -3.273 0.925 1.00 0.00 U C
ATOM 41 H81 MAC 0 6.081 -1.136 -0.148 1.00 0.00 U H
ATOM 42 H82 MAC 0 5.550 -2.185 -1.527 1.00 0.00 U H
ATOM 43 H83 MAC 0 6.270 -2.939 -0.032 1.00 0.00 U H
ATOM 44 H91 MAC 0 4.096 -2.858 1.910 1.00 0.00 U H
ATOM 45 H92 MAC 0 5.323 -3.895 1.040 1.00 0.00 U H
ATOM 46 H93 MAC 0 3.586 -3..909 0.524 1.00 0.00 U H
END

and here is the corresponding psf file is:

PSF

       6 !NTITLE
REMARKS original generated structure x-plor psf file
REMARKS 2 patches were applied to the molecule.
REMARKS topology my-top.inp
REMARKS segment U { first NTER; last CTER; auto angles dihedrals }
REMARKS defaultpatch NTER U:A 1
REMARKS defaultpatch CTER U:A 1

      46 !NATOM
       1 U A 1 MAC C CC 0.340000 12.0110 0
       2 U A 1 MAC OT1 OC -0.670000 15.9990 0
       3 U A 1 MAC OT2 OC -0.670000 15.9990 0
       4 U A 1 MAC N NH3 -0.300000 14.0070 0
       5 U A 1 MAC HT1 HC 0.330000 1.0080 0
       6 U A 1 MAC HT2 HC 0.330000 1.0080 0
       7 U A 1 MAC HT3 HC 0.330000 1.0080 0
       8 U A 1 MAC CA CT1 0..210000 12.0110 0
       9 U A 1 MAC HA HB 0.100000 1.0080 0
      10 U A 1 MAC N2 NH2 -0.470000 14.0070 0
      11 U A 1 MAC HA1 HB 0.310000 1.0080 0
      12 U A 1 MAC HA2 HB 0.090000 1.0080 0
      13 U A 1 MAC HA3 HB 0.000000 1.0080 0
      14 U A 1 MAC CB CA -0.180000 12.0110 0
      15 U A 1 MAC HB1 HB 0.090000 1.0080 0
      16 U A 1 MAC HB2 HB 0.090000 1..0080 0
      17 U A 1 MAC HB3 HB 0.000000 1.0080 0
      18 U A 1 MAC CD1 CA -0.115000 12.0110 0
      19 U A 1 MAC HD1 HP 0.115000 1.0080 0
      20 U A 1 MAC CE1 CA -0.115000 12.0110 0
      21 U A 1 MAC HE1 HP 0.115000 1.0080 0
      22 U A 1 MAC CZ CA 0.000000 12.0110 0
      23 U A 1 MAC CG CA 0.000000 12.0110 0
      24 U A 1 MAC CD2 CA -0.115000 12.0110 0
      25 U A 1 MAC HD2 HP 0.115000 1.0080 0
      26 U A 1 MAC CE2 CA 0.470000 12.0110 0
      27 U A 1 MAC C1 CA -0.115000 12.0110 0
      28 U A 1 MAC H1 HP 0.115000 1.0080 0
      29 U A 1 MAC C2 CA 0.000000 12.0110 0
      30 U A 1 MAC C3 CA 0.000000 12.0110 0
      31 U A 1 MAC C4 CA -0.115000 12.0110 0
      32 U A 1 MAC H4 HP 0.115000 1.0080 0
      33 U A 1 MAC C5 CA -0.115000 12.0110 0
      34 U A 1 MAC H5 HP 0.115000 1.0080 0
      35 U A 1 MAC C7 CA -0.115000 12.0110 0
      36 U A 1 MAC H7 HP 0.115000 1.0080 0
      37 U A 1 MAC C6 CA 0.070000 12.0110 0
      38 U A 1 MAC N1 NH2 -0.047000 14.0070 0
      39 U A 1 MAC C8 CA 0.080000 12.0110 0
      40 U A 1 MAC C9 CA 0.080000 12.0110 0
      41 U A 1 MAC H81 HB 0.040000 1.0080 0
      42 U A 1 MAC H82 HB 0.040000 1.0080 0
      43 U A 1 MAC H83 HB 0.040000 1.0080 0
      44 U A 1 MAC H91 HB 0.040000 1.0080 0
      45 U A 1 MAC H92 HB 0.040000 1.0080 0
      46 U A 1 MAC H93 HB 0.040000 1.0080 0

      46 !NBOND: bonds
       1 3 1 2 5 4 6 4
       7 4 8 11 8 12 8 13
      10 23 10 8 10 14 14 15
      14 16 14 17 18 19 18 20
      20 22 20 21 22 27 22 26
      23 18 23 24 24 25 26 24
      26 4 27 28 27 29 29 30
      29 31 30 4 31 32 31 33
      33 37 33 34 35 36 35 30
      37 35 38 37 38 39 38 40
      39 41 39 42 39 43 40 44
      40 45 40 46

      80 !NTHETA: angles
       3 1 2 4 26 22 5 4 30
       5 4 26 5 4 7 5 4 6
       6 4 30 6 4 26 6 4 7
       7 4 30 7 4 26 8 10 14
      10 23 24 10 14 17 10 14 16
      10 14 15 10 8 13 10 8 12
      10 8 11 11 8 13 11 8 12
      12 8 13 15 14 17 15 14 16
      16 14 17 18 23 24 18 23 10
      19 18 20 20 22 26 20 22 27
      21 20 18 22 27 29 22 27 28
      22 20 18 22 20 21 23 18 20
      23 18 19 23 10 14 23 10 8
      24 26 22 24 26 4 25 24 23
      26 24 23 26 24 25 26 4 30
      27 22 26 28 27 29 29 31 33
      29 31 32 29 30 4 29 30 35
      30 35 37 30 29 27 30 29 31
      31 29 27 32 31 33 33 37 35
      33 37 38 34 33 31 35 30 4
      36 35 37 36 35 30 37 38 40
      37 38 39 37 33 31 37 33 34
      38 40 46 38 40 45 38 40 44
      38 39 43 38 39 42 38 39 41
      38 37 35 39 38 40 41 39 43
      41 39 42 42 39 43 44 40 46
      44 40 45 45 40 46

     104 !NPHI: dihedrals
       4 30 29 31 4 30 29 27
       4 30 35 36 4 30 35 37
       4 26 24 25 4 26 24 23
       4 26 22 20 4 26 22 27
       5 4 26 24 5 4 26 22
       5 4 30 29 5 4 30 35
       6 4 26 24 6 4 26 22
       6 4 30 29 6 4 30 35
       7 4 26 24 7 4 26 22
       7 4 30 29 7 4 30 35
       8 10 23 18 8 10 23 24
       8 10 14 15 8 10 14 16
       8 10 14 17 10 23 18 19
      10 23 18 20 10 23 24 26
      10 23 24 25 11 8 10 23
      11 8 10 14 12 8 10 23
      12 8 10 14 13 8 10 23
      13 8 10 14 14 10 23 18
      14 10 23 24 15 14 10 23
      16 14 10 23 17 14 10 23
      18 23 24 26 18 23 24 25
      18 20 22 27 18 20 22 26
      19 18 23 24 19 18 20 22
      19 18 20 21 20 22 27 28
      20 22 27 29 20 22 26 24
      20 18 23 24 21 20 22 27
      21 20 22 26 21 20 18 23
      22 27 29 30 22 27 29 31
      22 26 24 25 22 26 24 23
      22 26 4 30 22 20 18 23
      24 26 4 30 24 26 22 27
      26 22 27 28 26 22 27 29
      26 4 30 29 26 4 30 35
      27 29 30 35 27 29 31 32
      27 29 31 33 28 27 29 30
      28 27 29 31 29 31 33 37
      29 31 33 34 29 30 35 36
      29 30 35 37 30 35 37 33
      30 35 37 38 30 29 31 32
      30 29 31 33 31 33 37 38
      31 33 37 35 31 29 30 35
      32 31 33 37 32 31 33 34
      33 37 38 39 33 37 38 40
      33 37 35 36 34 33 37 38
      34 33 37 35 35 37 38 39
      35 37 38 40 36 35 37 38
      37 38 39 41 37 38 39 42
      37 38 39 43 37 38 40 44
      37 38 40 45 37 38 40 46
      39 38 40 44 39 38 40 45
      39 38 40 46 40 38 39 41
      40 38 39 42 40 38 39 43

       1 !NIMPHI: impropers
       1 8 3 2

       0 !NDON: donors

       0 !NACC: acceptors

       0 !NNB

       0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0
       0 0 0 0 0 0

       1 0 !NGRP
       0 0 0

plz help

-- 
Rudra
JRF; SNBNCBS
http://www.bose.res.in/~rudra
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