Re: [AMBER] sander API data structure

From: Daniel Roe <>
Date: Tue, 16 May 2017 11:03:21 -0400


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.


On Tue, May 16, 2017 at 9:43 AM, Brent Krueger <> 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. 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
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Received on Tue May 16 2017 - 08:30:02 PDT
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