[gmx-developers] Reading unprocessed topology files

[Mark Abraham]

On Mon, May 27, 2013 at 6:04 PM, Roland Schulz <roland at utk.edu> wrote:

> On Mon, May 27, 2013 at 9:56 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > On Mon, May 27, 2013 at 3:40 AM, Pedro Lacerda <kanvuanza+gmx at zoho.com>
>
> >> ## The question:
> >> How can I read an topology file for populate my t_atoms (or gmx_mtop_t)
> >> with eg. charges and masses? read_tpx() in tpxio.h can use only
> preprocessed
> >> file formats like TPR. do_top() in topio.h seems a bit exagerated (in
> number
> >> of function parameters) to just parse an TOP or ITP file and populate
> some
> >> objects. If do_top() is the way to go, is grompp's new_status() approach
> >> reasonable?
> >
> >
> > The lack of modularity in this code is its most obvious quality. My usual
> > recommendation for these kinds of questions is to pick a GROMACS tool
> that
> > does something close to what you want, look at how it populates a data
> > structure, do the same thing, and work out how to get the subset of data
> you
> > really want. new_status() probably (over-)fills your needs.
>
> Do we have analysis tools which read topology from a top/itp file? I
> thought analysis tools always read it from the TPR.
>

IIRC genion touches the .top file, but I don't know if it parses much.

Mark

@Pedro: What is the reason you need to read a top file, and cannot
> generate a tpr first and then read it?
>
> Roland
>
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