VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 22 2008 - 23:59:54 CDT

Rudra,
  Can you try one of the test versions of VMD 1.8.7 and let me know
if you're still experiencing this problem? Also, how much memory does
your machine have in it, and how large is thr structure you're
working on?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 23, 2008 at 10:22:34AM +0530, Rudra Banerjee wrote:
> Dear friends,
>
>
>
> 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), the vmd is crashing without giving any error /log..
> hence i am not getting any clue about what is going wrong and hence in big dig.plz help..
>
> i am using the command
> $package require solvate
> $solvate aoq.psf aoq.pdb -t 10 -o aoq_wb
>
> this type of command is working for other molecule but this time its breaking.
> as for my os is ocncerned:
> Linux snbpc30.lan.bose.res.in 2.6.25.14-69.fc8 #1 SMP Mon Aug 4 14:20:24 EDT 2008 i686 i686 i386 GNU/Linux.
>
> 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
> >
> >
> Another question is: the do atoms with occupancy -1 affect the simulation at all?
> > --
> > Rudra
> > JRF; SNBNCBS
> > http://www.bose.res.in/~rudra
> >
> > A bus station is where a bus stops. A train station is where a train
> > stops. On my desk I have a work station.
> >
> > Please, if possible, don't send me MS Word or PowerPoint attachments
> > Why?See: http://www.gnu.org/philosophy/no-word-attachments.html
> >
>
>
> Cricket on your mind? Visit the ultimate cricket website. Enter http://in.sports.yahoo.com/cricket/
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078