On Mon, Oct 31, 2011 at 9:45 AM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Mon, Oct 31, 2011 at 8:29 AM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Sun, Oct 30, 2011, Gonzalo Jimenez wrote:
>>
>> > I guess the reason is that tLEAP renumbers the atoms based on
>> > connectivities, but if I cannot circunvent this default option, I
>> > basically cannot run TI, right?
>>
>> The replies given by Jason and Thomas are good ones, but I'm pretty sure
>> tleap
>> does not change the order of atoms given in the library file you import.
>> Maybe if you give an example of exactly what you are seeing, we could say
>> more.
>>
>
> No, but a "copy" command will actually change the orders of the pointer
> arrays in tleap -- I'm not sure what effect this would have (if any).
>
> However, if you compare 2 topologies created via:
>
> l = sequence {NALA ALA ALA CALA}
> k = copy l
> saveamberparm l l.prm
> saveamberparm k.prm
>
Just don't butcher the saveamberparm syntax here :)
saveamberparm l l.prm l.crd
saveamberparm k k.prm k.crd
>
> If you then diff the 2, you'll see a ton of differences. I'm not sure if
> this will give the TI code a hard time or not (obviously it'd be ideal if
> the bond/angle/dihedral calculations were order-independent in each group,
> but I haven't looked at the code closely enough to be sure of that).
>
> All the best,
> Jason
>
>
>> ...dac
>>
>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 31 2011 - 07:00:04 PDT
