VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 25 2008 - 08:12:34 CDT

Hi Rudra,
it appears that your psf has an extra column in it, which is breaking
the reader. If you delete the third field of each of the atom entries in
the psf (the A, which shouldn't be there) things work fine. I'm
attaching a corrected version. You also need to change the resid of your
residue in the pdb file from 0 to 1 in order to match the psf. Do you
have any idea how this extra column showed up? Could you tar your
original pdb, psfgen input, and topology file and send them to me?
Peter

Rudra Banerjee wrote:
> 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.
>
>
>


  • application/octet-stream attachment: mac.tbz