i don't think you can presently take the extended chain and use TMD to make
it fold- not for something this large. the problems is that it will become
compact and then to get it properly folded it will likely need to unfold and
re-collapse many times (since chains can't pass through each other). doing
folding using MD is very difficult- even with many restraints.
if it's just for aesthetics, I suggest taking the known structure and then
heating it in MD until it unfolds, then run the trajectory reverse in time
for making the movie. it's not the right science, but just for a movie
you'll save huge effort..
On Thu, Oct 28, 2010 at 2:25 PM, Jordan, Brad <jbjordan.amgen.com> wrote:
> Hi - I'm trying to simulate the folding of a protein (for purely aesthetic
> reasons) and was hoping to use AMBER to do this from an extended strand
> structure. The protein is around 160 amino acids. I actually took the
> crystal structure of the folded protein and generated around 20K NMR-type
> distance restraints. I was hoping to use targeted MD to do this using the
> crystal structure as the target structure. Does anyone have a sense of
> whether this will work or not? Initially, I'm attempting to minimize the
> extended strand starting structure as done in Ross Walker's tutorial, but it
> seems that the system may be too big. Any ideas would be greatly
> appreciated.
>
> Thanks,
>
> Brad
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 28 2010 - 12:00:03 PDT
