For now, I think the easiest way is to use sander Python API with
ParmEd's AmberParm. Under the hood, ParmEd save its object to prmtop
file and then passing to pysander.
https://github.com/Amber-MD/pysander/blob/master/sander/__init__.py#L275
Of couse, we need to build ParmEd's AmberParm (either via tleap or
construct it in memory)
Hai
On Tue, May 16, 2017 at 11:03 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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 - 09:00:03 PDT
