input coordinates & charges

Axel akoh... at
Wed May 7 17:00:05 UTC 2008

dear csilla,

On May 7, 11:55 am, Csilla Varnai <cv... at> wrote:
> Dear all,
> I am trying to read a small peptide to run an MD calculation. I cannot
> define the atomic charges in the FORCEFIELD section, because there is
> no one-to-one mapping between the atomic types and the atomic charges
> in case of peptides. Hence, I need to read in the charges. I have

i'm a bit confused as to why you want to manually enter
all the topology parameters? why don't you just use a
tool like psfgen from VMD/NAMD to build a .psf file that
contains all the information more or less automatically?


> found only 1 way to do it so far, namely reading it from a PDB file.
> My problem is that in this case I loose the accuracy of the
> coordinates, since this format is fairly restricted and I cannot read
> the coordinates only at a +/-0.001 level.
> Could anyone please help me, if there is a better way I've missed to
> get both the charges and the coordinates at a given accuracy?
> Thanks very much,
> Csilla
>  cp2k.inp
> 1KDownload

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