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
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
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Received on Mon Oct 31 2011 - 07:00:03 PDT
