[CP2K:2901] About cp2k problem

[Toon Verstraelen]

On 11/03/2010 12:57 AM, Buddhadev Maiti wrote:
> I am performing MD simulation using cp2k. I have a question regarding
> input file preparation. I am reading coordinates from PDB file and using
> amber force field. I would like water to be rigid during simulation.
> What will be the suitable keyword in MOLNAME option, it will be great
> help for me. Because in PDB file there is no MOL keyword.
>
> &CONSTRAINT
> &G3X3
>        EXCLUDE_QM
>        DISTANCES 1.8896447 1.8896447 3.0862864
>        MOLNAME ????
>        ATOMS 1 2 3
> &END G3X3
> &END
>
> PDB file of WATER looks like:
>
> ATOM  32914  H1  WAT  9851     -37.475 -29.571 -27.585  1.00  0.00
> ATOM  32915  H2  WAT  9851     -37.251 -29.868 -26.118  1.00  0.00
> ATOM  32916  O   WAT  9851     -37.763 -29.316 -26.708  1.00  0.00
> TER
> ATOM  32917  H1  WAT  9852     -36.769 -28.630 -19.298  1.00  0.00
> ATOM  32918  H2  WAT  9852     -37.711 -27.567 -19.823  1.00  0.00
> ATOM  32919  O   WAT  9852     -37.696 -28.394 -19.341  1.00  0.00
>

I think CP2K uses the resname if there is no vmd-style (col 73:76) 
molname in the pdb file. Normally one also includes a topology file 
(e.g. .psf file) which contains the molecule specifications.

I can only tell for sure in your case when you provide the complete 
input files. Please include all and entire input files in the 
attachments. That makes it a lot easier to help you.

cheers,

Toon