> could someone point me to the relevant lines of code that write amber
topology files?
leap: unitio.c zUnitIOSaveAmberParmFormat
Bill
On 5/16/17 9:15 AM, Brent Krueger wrote:
> Thank you Hai and Dan.
>
> My goal was to avoid ever writing the topology file to disk, but it sounds
> like that is not possible. Probably, then, we'll just write the topology
> file ourselves.
>
> I'm sure we can build this from the topology file format definition on the
> amber site, but could someone point me to the relevant lines of code that
> write amber topology files? Those will surely be a time-saver.
>
>
> Thanks,
> Brent
>
>
> On Tue, May 16, 2017 at 11:32 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue May 16 2017 - 11:00:03 PDT
