VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Feb 25 2011 - 08:55:47 CST

Hi Sebastian,

Your topology file is not being parsed correctly. Not sure why, but
you could check it for inconspicuous special characters, including the
end-of-line characters (are they a mixture of DOS and UNIX-style?).
Also, psfgen only handles one set of coordinates. You can load the
PSF, then the original PDB file into VMD (not psfgen), then you can
save all frames to whatever format you like.

Best,
Jerome

On 25 February 2011 12:30, Sebastian Maximilian Wilhelm
<Sebastian.Wilhelm_at_rwth-aachen.de> wrote:
> Hi,
>
> I tried to write my own topo-file for a methanol TOPMethanol.inp:
>
> * Topology file for Methanol
> *
> *
> MASS     1 CH3   15.03500  CH3  ! site CH3
> MASS     2 OS    15.99900  O    ! hydroxyl oxygen
> MASS     3 HS     1.00800  H      ! hydroxyl hydrogen
>
> RESI ME         0.00
> AUTO ANGLES               !
>                          !
> GROUP
>                          !   C3--O
> ATOM C3    CH3      0.32  !        \
> ATOM O     OS      -0.66  !         H
> ATOM H     HS       0.34
> BOND C3 O  O H
>
>
> END
>
> I扉e read that it is not absolute essential to write the ICs if all molecules and their positions are available from the .pdb-file. I have converted a .pdb-file for the trajectories (400 frames) of 4 methanol molecules (Methanol1234.pdb):
>
> CRYST1   64.750   64.750   64.750  90.00  90.00  90.00 P 1           1
> ATOM      1  C3  ME  X   1       4.876 -24.666 -17.653  0.00  0.00
> ATOM      2  O   ME  X   1       4.114 -25.506 -18.524  0.00  0.00
> ATOM      3  H   ME  X   1       3.287 -25.047 -18.532  0.00  0.00
> ATOM      4  C3  ME  X   2       2.657  -3.561 -14.849  0.00  0.00
> ATOM      5  O   ME  X   2       2.210  -4.727 -15.547  0.00  0.00
> ATOM      6  H   ME  X   2       2.414  -4.630 -16.465  0.00  0.00
> ATOM      7  C3  ME  X   3     -18.595  28.600 -32.029  0.00  0.00
> ATOM      8  O   ME  X   3     -17.593  27.584 -31.955  0.00  0.00
> ATOM      9  H   ME  X   3     -17.643  27.227 -31.081  0.00  0.00
> ATOM     10  C3  ME  X   4     -29.535 -26.831 -25.221  0.00  0.00
> ATOM     11  O   ME  X   4     -29.762 -26.388 -23.880  0.00  0.00
> ATOM     12  H   ME  X   4     -29.500 -27.099 -23.316  0.00  0.00
> END
> (my comment: next frame)
> ATOM      1  C3  ME  X   1       4.875 -24.695 -17.615  0.00  0.00
> ATOM      2  O   ME  X   1       4.118 -25.488 -18.534  0.00  0.00
> ATOM      3  H   ME  X   1       3.295 -25.025 -18.509  0.00  0.00
> ATOM      4  C3  ME  X   2       2.657  -3.566 -14.850  0.00  0.00
> ATOM      5  O   ME  X   2       2.234  -4.733 -15.559  0.00  0.00
> ATOM      6  H   ME  X   2       2.428  -4.601 -16.475  0.00  0.00
> ATOM      7  C3  ME  X   3     -18.614  28.585 -32.030  0.00  0.00
> ATOM      8  O   ME  X   3     -17.576  27.603 -31.968  0.00  0.00
> ATOM      9  H   ME  X   3     -17.584  27.244 -31.094  0.00  0.00
> ATOM     10  C3  ME  X   4     -29.531 -26.845 -25.227  0.00  0.00
> ATOM     11  O   ME  X   4     -29.757 -26.391 -23.891  0.00  0.00
> ATOM     12  H   ME  X   4     -29.458 -27.060 -23.294  0.00  0.00
> END
> .
> .
> .
>
> and the script out of the NAMD tutorial for creating .psf adapted to my specifications:
>
> package require psfgen
> topology TOPMethanol.inp
> segment Al {pdb Methanol1234.pdb}
> coordpdb Methanol1234.pdb Al
> writepdb PDBMethanol.pdb
> writepsf PSFMethanol.psf
>
> If I execute this script in the VMD Tk console, four warnings occur: failed to set coordinate for atom C3 in ME1, ME2, ME3, ME4. Anyway, the .pdb and the .psf files are written, but in the PDBMethanol.pdb-file no coordinates for C3 are entered:
>
> REMARK original generated coordinate pdb file
> ATOM      1  O   ME  X   1       4.114 -25.506 -18.524  1.00  0.00      AL   O
> ATOM      2  H   ME  X   1       3.287 -25.047 -18.532  1.00  0.00      AL   H
> ATOM      3  O   ME  X   2       2.210  -4.727 -15.547  1.00  0.00      AL   O
> ATOM      4  H   ME  X   2       2.414  -4.630 -16.465  1.00  0.00      AL   H
> ATOM      5  O   ME  X   3     -17.593  27.584 -31.955  1.00  0.00      AL   O
> ATOM      6  H   ME  X   3     -17.643  27.227 -31.081  1.00  0.00      AL   H
> ATOM      7  O   ME  X   4     -29.762 -26.388 -23.880  1.00  0.00      AL   O
> ATOM      8  H   ME  X   4     -29.500 -27.099 -23.316  1.00  0.00      AL   H
> END
>
>
> and in the .psf-file, no C3 occurs:
> PSF
>
>       3 !NTITLE
>  REMARKS original generated structure x-plor psf file
>  REMARKS topology TOPMethanol.inp
>  REMARKS segment AL { first NONE; last NONE; auto angles  }
>
>       8 !NATOM
>       1 AL   1    ME   O    OS    -0.660000       15.9990           0
>       2 AL   1    ME   H    HS     0.340000        1.0080           0
>       3 AL   2    ME   O    OS    -0.660000       15.9990           0
>       4 AL   2    ME   H    HS     0.340000        1.0080           0
>       5 AL   3    ME   O    OS    -0.660000       15.9990           0
>       6 AL   3    ME   H    HS     0.340000        1.0080           0
>       7 AL   4    ME   O    OS    -0.660000       15.9990           0
>       8 AL   4    ME   H    HS     0.340000        1.0080           0
>
>       0 !NBOND: bonds
>
>
>       0 !NTHETA: angles
>
>
>       0 !NPHI: dihedrals
> Now, I have two questions:
> -why is C3 ignored? I tried changing the name into CH3, only C or even totally different like A1 (of course in the original .pdb and in the topology-file), but nothing has changed.
> -why is only one frame instead of 400 written?
>
> Thanks for your help!
>
> Best regards,
> Sebastian
>
>
>