VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Dec 05 2009 - 08:21:29 CST

Hi Francesco,
did you use a CG topology file? It looks like you tried to use an all
atom topology file with your CG protein, which is not going to work...
Best,
Peter

Francesco Pietra wrote:
> 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
>