Hi,
I don't think passing topology parameters directly is officially
supported. A brief glance through sander.h shows that there is what
looks like a topology structure and corresponding function calls:
struct: prmtop_struct
functions: sander_setup2 (2 versions)
However, they don't appear to be documented or tested, so I would use
these with extreme caution.
FWIW, cpptraj makes use of the sander API by using the "officially"
supported method of passing in a topology name. Since this only has to
be done once the actual overhead is minimal since the topology stays
in memory after the setup call.
-Dan
On Tue, May 16, 2017 at 9:43 AM, Brent Krueger <kruegerb.hope.edu> wrote:
> We would like to use the sander API to do some energy evaluation of some
> simple systems. Part of the goal is to avoid lots of unnecessary disk I/O.
>
> Therefore, we would like to create topology and coordinate information
> within our own program and keep it resident in memory. The coordinates are
> easy enough, but I don't see anything in the manual about what data
> structure holds the topology information and how we can access it. All of
> the examples simply use the sander_setup_mm() function to read a topology
> file from disk.
>
> Maybe there are too many idiosyncrasies in the topology construction and we
> should just go ahead and use leap or parmed to do that. But our situation
> is very simple, We are modeling a crystal lattice, so there are no bonds
> just some ions with VDW parameters and charges. I feel like this is simple
> enough that we ought to be able to create this ourselves and pass it to the
> sander API.
>
> Any information or examples would be appreciated. Oh, and we are using C,
> but I suppose we could use anything else if that would make life easier.
>
>
> Thanks,
> Brent
>
> --
> _______________________________________________
> Brent P. Krueger.....................phone: 616 395 7629
> Professor.................................fax: 616 395 7118
> Hope College..........................Schaap Hall 2120
> Department of Chemistry
> Holland, MI 49423
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue May 16 2017 - 08:30:02 PDT
