VMD-L Mailing List

From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Wed Sep 24 2008 - 23:42:22 CDT

and also, i should give the generated pdb and psf file:
the generated pdb file is(aoq.pdb):
REMARK original generated coordinate pdb file
ATOM 1 N2 MAC 0 -4.299 0.713 1.207 1.00 0.00 U N
ATOM 2 HA1 MAC 0 -5.986 1.045 1.614 1.00 0.00 U H
ATOM 3 CA MAC 0 -5.107 1.352 1.005 1.00 0.00 U C
ATOM 4 HA2 MAC 0 -4.830 2.397 1.270 1.00 0..00 U H
ATOM 5 HA3 MAC 0 -5.354 1.307 -0.080 1..00 0.00 U H
ATOM 6 CB MAC 0 -4.392 -0.073 1.897 1.00 0.00 U C
ATOM 7 HB1 MAC 0 -3.663 0.071 2.725 1.00 0.00 U H
ATOM 8 HB2 MAC 0 -5.425 -0.085 2.310 1.00 0.00 U H
ATOM 9 HB3 MAC 0 -4.187 -1.041 1.386 1.00 0.00 U H
ATOM 10 CD1 MAC 0 -3.039 1.934 -0.283 1.00 0.00 U C
ATOM 11 HD1 MAC 0 -3.879 2.612 -0.492 1.00 0.00 U H
ATOM 12 CE1 MAC 0 -1.812 2.120 -0.917 1.00 0.00 U C
ATOM 13 HE1 MAC 0 -1.685 2.949 -1.629 1.00 0.00 U H
ATOM 14 CZ MAC 0 -0.733 1.261 -0.643 1.00 0.00 U C
ATOM 15 CG MAC 0 -3.189 0.892 0.625 1.00 0.00 U C
ATOM 16 CD2 MAC 0 -2.112 0.042 0.894 1.00 0.00 U C
ATOM 17 HD2 MAC 0 -2.248 -0.784 1.607 1.00 0.00 U H
ATOM 18 CE2 MAC 0 -0.879 0.204 0.276 1.00 0.00 U C
ATOM 19 N MAC 0 0.123 -0.642 0.571 1.00 0.00 U N
ATOM 20 C1 MAC 0 0.512 1..419 -1.262 1.00 0.00 U C
ATOM 21 H1 MAC 0 0.669 2.239 -1.978 1.00 0.00 U H
ATOM 22 C2 MAC 0 1.562 0.544 -0.962 1.00 0.00 U C
ATOM 23 C3 MAC 0 1.315 -0.482 -0.029 1.00 0.00 U C
ATOM 24 C4 MAC 0 2.827 0.670 -1.563 1.00 0.00 U C
ATOM 25 H4 MAC 0 3.013 1.474 -2.290 1.00 0.00 U H
ATOM 26 C5 MAC 0 3.854 -0.212 -1.232 1.00 0.00 U C
ATOM 27 H5 MAC 0 4.846 -0.106 -1.696 1.00 0.00 U H
ATOM 28 C7 MAC 0 2.353 -1.354 0.273 1.00 0.00 U C
ATOM 29 H7 MAC 0 2.175 -2.167 0.992 1.00 0..00 U H
ATOM 30 C6 MAC 0 3.613 -1.234 -0.321 1..00 0.00 U C
ATOM 31 N1 MAC 0 4.671 -2.189 0.006 1.00 0.00 U N
ATOM 32 C8 MAC 0 5.628 -2.116 -0.419 1.00 0.00 U C
ATOM 33 C9 MAC 0 4.407 -3.273 0.925 1.00 0.00 U C
ATOM 34 H81 MAC 0 6.081 -1.136 -0.148 1.00 0.00 U H
ATOM 35 H82 MAC 0 5.550 -2.185 -1.527 1.00 0.00 U H
ATOM 36 H83 MAC 0 6.270 -2.939 -0.032 1.00 0.00 U H
ATOM 37 H91 MAC 0 4.096 -2.858 1.910 1.00 0.00 U H
ATOM 38 H92 MAC 0 5.323 -3.895 1.040 1.00 0.00 U H
ATOM 39 H93 MAC 0 3.586 -3.909 0.524 1.00 0.00 U H
END

and the psf file is(aoq.psf):
PSF

       3 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS topology my-top.inp
 REMARKS segment U { first NONE; last NONE; auto angles dihedrals }

      39 !NATOM
       1 U A 1 MAC N2 NH2 -0.470000 14.0070 0
       2 U A 1 MAC HA1 HB 0.310000 1.0080 0
       3 U A 1 MAC CA CA 0.070000 12..0110 0
       4 U A 1 MAC HA2 HB 0.090000 1.0080 0
       5 U A 1 MAC HA3 HB 0.000000 1.0080 0
       6 U A 1 MAC CB CA -0.180000 12.0110 0
       7 U A 1 MAC HB1 HB 0.090000 1.0080 0
       8 U A 1 MAC HB2 HB 0.090000 1.0080 0
       9 U A 1 MAC HB3 HB 0.000000 1.0080 0
      10 U A 1 MAC CD1 CA -0.115000 12.0110 0
      11 U A 1 MAC HD1 HP 0.115000 1.0080 0
      12 U A 1 MAC CE1 CA -0.115000 12.0110 0
      13 U A 1 MAC HE1 HP 0.115000 1.0080 0
      14 U A 1 MAC CZ CA 0.000000 12.0110 0
      15 U A 1 MAC CG CA 0.000000 12.0110 0
      16 U A 1 MAC CD2 CA -0.115000 12.0110 0
      17 U A 1 MAC HD2 HP 0.115000 1.0080 0
      18 U A 1 MAC CE2 CA 0.470000 12.0110 0
      19 U A 1 MAC N N -0.470000 14.0070 0
      20 U A 1 MAC C1 CA -0.115000 12.0110 0
      21 U A 1 MAC H1 HP 0.115000 1.0080 0
      22 U A 1 MAC C2 CA 0.000000 12.0110 0
      23 U A 1 MAC C3 CA 0.000000 12.0110 0
      24 U A 1 MAC C4 CA -0.115000 12.0110 0
      25 U A 1 MAC H4 HP 0.115000 1.0080 0
      26 U A 1 MAC C5 CA -0.115000 12.0110 0
      27 U A 1 MAC H5 HP 0.115000 1.0080 0
      28 U A 1 MAC C7 CA -0.115000 12.0110 0
      29 U A 1 MAC H7 HP 0.115000 1.0080 0
      30 U A 1 MAC C6 CA 0.070000 12.0110 0
      31 U A 1 MAC N1 NH2 -0.047000 14.0070 0
      32 U A 1 MAC C8 CA 0.080000 12.0110 0
      33 U A 1 MAC C9 CA 0.080000 12.0110 0
      34 U A 1 MAC H81 HB 0.040000 1.0080 0
      35 U A 1 MAC H82 HB 0.040000 1.0080 0
      36 U A 1 MAC H83 HB 0.040000 1.0080 0
      37 U A 1 MAC H91 HB 0.040000 1.0080 0
      38 U A 1 MAC H92 HB 0.040000 1.0080 0
      39 U A 1 MAC H93 HB 0.040000 1.0080 0

      41 !NBOND: bonds
       1 15 1 3 1 6 3 2
       3 4 3 5 6 7 6 8
       6 9 10 11 10 12 12 14
      12 13 14 20 14 18 15 10
      15 16 16 17 18 16 18 19
      20 21 20 22 22 23 22 24
      23 19 24 25 24 26 26 30
      26 27 28 29 28 23 30 28
      31 30 31 32 31 33 32 34
      32 35 32 36 33 37 33 38
      33 39

      70 !NTHETA: angles
       1 15 16 1 6 9 1 6 8
       1 6 7 1 3 5 1 3 4
       1 3 2 2 3 5 2 3 4
       3 1 6 4 3 5 7 6 9
       7 6 8 8 6 9 10 15 16
      10 15 1 11 10 12 12 14 18
      12 14 20 13 12 10 14 20 22
      14 20 21 14 12 10 14 12 13
      15 10 12 15 10 11 15 1 6
      15 1 3 16 18 14 16 18 19
      17 16 15 18 19 23 18 16 15
      18 16 17 19 18 14 20 14 18
      21 20 22 22 24 26 22 24 25
      22 23 19 22 23 28 23 28 30
      23 22 20 23 22 24 24 22 20
      25 24 26 26 30 28 26 30 31
      27 26 24 28 23 19 29 28 30
      29 28 23 30 31 33 30 31 32
      30 26 24 30 26 27 31 33 39
      31 33 38 31 33 37 31 32 36
      31 32 35 31 32 34 31 30 28
      32 31 33 34 32 36 34 32 35
      35 32 36 37 33 39 37 33 38
      38 33 39

      92 !NPHI: dihedrals
       1 15 10 11 1 15 10 12
       1 15 16 18 1 15 16 17
       2 3 1 15 2 3 1 6
       3 1 15 10 3 1 15 16
       3 1 6 7 3 1 6 8
       3 1 6 9 4 3 1 15
       4 3 1 6 5 3 1 15
       5 3 1 6 6 1 15 10
       6 1 15 16 7 6 1 15
       8 6 1 15 9 6 1 15
      10 15 16 18 10 15 16 17
      10 12 14 20 10 12 14 18
      11 10 15 16 11 10 12 14
      11 10 12 13 12 14 20 21
      12 14 20 22 12 14 18 16
      12 14 18 19 12 10 15 16
      13 12 14 20 13 12 14 18
      13 12 10 15 14 20 22 23
      14 20 22 24 14 18 16 17
      14 18 16 15 14 18 19 23
      14 12 10 15 15 16 18 19
      16 18 19 23 16 18 14 20
      17 16 18 19 18 19 23 22
      18 19 23 28 18 14 20 21
      18 14 20 22 19 23 22 24
      19 23 22 20 19 23 28 29
      19 23 28 30 19 18 14 20
      20 22 23 28 20 22 24 25
      20 22 24 26 21 20 22 23
      21 20 22 24 22 24 26 30
      22 24 26 27 22 23 28 29
      22 23 28 30 23 28 30 26
      23 28 30 31 23 22 24 25
      23 22 24 26 24 26 30 31
      24 26 30 28 24 22 23 28
      25 24 26 30 25 24 26 27
      26 30 31 32 26 30 31 33
      26 30 28 29 27 26 30 31
      27 26 30 28 28 30 31 32
      28 30 31 33 29 28 30 31
      30 31 32 34 30 31 32 35
      30 31 32 36 30 31 33 37
      30 31 33 38 30 31 33 39
      32 31 33 37 32 31 33 38
      32 31 33 39 33 31 32 34
      33 31 32 35 33 31 32 36

       0 !NIMPHI: impropers

       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

       1 0 !NGRP
       0 0 0

and once again, for the sake of completness, the error while i am trying to solvate the molecule is:

Main console display active (Tcl8.4.1 / Tk8.4.1)
(ao) 1 % package require solvate
1.2
>Main< (ao) 2 % solvate aoq.psf aoq.pdb -t 25 -o aoq_wb
reading structure from psf file aoq.psf
error reading atoms

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

  

-- 
Rudra
JRF; SNBNCBS
http://www.bose.res.in/~rudra
A bus station is where a bus stops. A train station is where a train
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Why?See:  http://www.gnu.org/philosophy/no-word-attachments.html
----- Original Message ----
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
To: Rudra Banerjee <bnrj.rudra_at_yahoo.com>
Cc: vmd-l_at_ks.uiuc.edu
Sent: Thursday, 25 September, 2008 9:31:48 AM
Subject: Re: vmd-l: psf file generation: once again
The solution was suggested by Christopher Chang yesterday: turn off 
automatic patching.
segment U {
pdb blah.pdb
first none
last none
}
      Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/