VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Tue Sep 23 2008 - 11:57:58 CDT

Rudra,

   Also, there are seven atoms sitting on top of each other at the origin; I
am guessing this resulted from unsuccessful (and unintentional) N- and
C-terminal patches. Make sure to turn patching off for this custom molecule,
otherwise it will be treated as an amino acid by default.

On 9/22/08 11:01 PM, "Rudra Banerjee" <bnrj.rudra_at_yahoo.com> wrote:

> 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 

-- 
Christopher H. Chang, Ph.D.
Scientist II
National Renewable Energy Laboratory
1617 Cole Blvd., MS 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007