VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Dec 04 2009 - 12:35:12 CST

Hi:
I wonder whether by simply showing sections of an input
cg-protein-bilayer.pdb may suggest why the resulting pdb has zero
value for all coordinates, while the psf was formed. I used VMD 1.8.7
with the Nov 5, 2009 version of autopsf.tcl (sourced before using
AutoPSF, and used successfully with the cg-protein.pdb alone).

Start of file:

ATOM      1  BB  LEU A   1      94.117   6.647  33.003  1.00  0.00           C
ATOM      2 LEU2 LEU A   1      91.702   4.673  31.893  1.00  0.00           C
ATOM      3  BB  SER A   2      96.602   4.840  33.767  1.00  0.00           C

......................

End 1st subunit and start of 2nd (similarly for the other subunits):

ATOM    834 LYS2 LYS A 426      87.486  15.560  52.901  1.00  0.00           C
ATOM    836  BB  LEU B   1      63.700  14.066  32.470  1.00  0.00           C
ATOM    837 LEU2 LEU B   1      62.820  11.464  34.800  1.00  0.00           C
ATOM    838  BB  SER B   2      66.653  14.844  33.474  1.00  0.00           C
ATOM    839 SER2 SER B   2      66.910  16.287  35.447  1.00  0.00           C

.........................

End of protein and start of lipid:

ATOM   2484 ALA2 ALA C 419     100.557  15.272  22.450  1.00  0.00           C
ATOM   2485  BB  TYR C 420      99.103  10.800  24.846  1.00  0.00           C
ATOM   2486 TYR2 TYR C 420     101.793  14.152  26.627  1.00  0.00           C
ATOM      1 CHO  POPCL   1      45.698  63.146   8.734  1.00  0.00           N
ATOM      2 PHO  POPCL   1      48.402  64.504   6.458  1.00  0.00           P
ATOM      3 ES1  POPCL   1      49.993  59.387   4.107  1.00  0.00           C

It may be noticed that the lipid atom name is placed at 13,14,15 while
in cg.membrane obtained with VMD is at 14,15,16. Actually, I combined
protein and membrane (and removed clashes) outside VMD (in the past I
was unable to do so with VMD).
..................................

"Interface" lipid-water:

ATOM   2728 ME6  POPCL  19     109.251  34.896  60.703  1.00  0.00           C
ATOM   2729 MT2  POPCL  19     107.211  38.181  61.495  1.00  0.00           C
ATOM   2730 H2O  TIP3W   2     132.301  54.580  49.722  1.00  0.00           O
ATOM   2731 H2O  TIP3W  22     130.101  22.103  32.812  1.00  0.00           O
ATOM   2732 H2O  TIP3W  35     109.445  25.664  35.058  1.00  0.00           O

.....................

End of file:

ATOM   3043 H2O  TIP3W4585     112.752  66.685  58.218  1.00  0.00           O
ATOM   3044 H2O  TIP3W4966     109.811  68.176  58.019  1.00  0.00           O
END
=================

The output pdb:

ATOM      1  N   LEU A   1       0.000   0.000   0.000 -1.00  0.00      P1   N
ATOM      2  HN  LEU A   1       0.000   0.000   0.000 -1.00  0.00      P1   H
ATOM      3  CA  LEU A   1       0.000   0.000   0.000 -1.00  0.00      P1   C

The output psf:

PSF CMAP

     40 !NTITLE
REMARKS original generated structure x-plor psf file
REMARKS topology popc+mod21_autopsf-temp.top
REMARKS segment P1 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment P2 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment P3 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O1 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O2 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O3 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O4 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O5 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O6 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O7 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O8 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment W1 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O9 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O10 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O11 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O12 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O13 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O14 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O15 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O16 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O17 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O18 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment W2 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O19 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O20 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O21 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O22 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O23 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O24 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment W3 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O25 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O26 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O27 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O28 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O29 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O30 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O31 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment W4 { first NONE; last NONE; auto angles dihedrals }

  41610 !NATOM
      1 P1   1    LEU  N    NH1   -0.470000       14.0070           0
      2 P1   1    LEU  HN   H      0.310000        1.0080           0
      3 P1   1    LEU  CA   CT1    0.070000       12.0110           0
      4 P1   1    LEU  HA   HB     0.090000        1.0080           0
      5 P1   1    LEU  CB   CT2   -0.180000       12.0110           0
      6 P1   1    LEU  HB1  HA     0.090000        1.0080           0
      7 P1   1    LEU  HB2  HA     0.090000        1.0080           0
      8 P1   1    LEU  CG   CT1   -0.090000       12.0110           0
      9 P1   1    LEU  HG   HA     0.090000        1.0080           0
.........................
..................
===============

Of course, this psf does not match with the input pdb.
=========

thanks
francesco pietra