On Thu, Sep 21, 2017, Rana Rehan Khalid wrote:
> Hi, Our system consist of two fragments, one have 324 residues while
> other fragment consist 43 A.A residues. I want to study the conformation
> changes when the smaller fragment of amino acids docked with the larger
> fragment. how i manage these two fragment in the single pdb file.
It's very hard to tell what sort of structural information you have. MD
simulations (in Amber or any other program) require a set of starting
coordinates. If you know how the smaller fragment fits into the larger one,
then use those coordinates.
If you need to "dock" the smaller fragment onto the larger one (e.g. you
know the conformations of both fragements but not how the fit together), you
will need to you some other software to get a good starting configuraion.
This might be "docking" software or "homology building" software, depending
on your problems.
If you don't know the conformation of the smaller (43 aa) fragment, then
you may be facing an intractable problem.
I'm being a bit long-winded here, to try to illustrate the reasons why it
is difficult for people on the list to be of very much help: without a *lot*
more information about what is known and not known about your system, people
don't even know where to start in providing help.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 21 2017 - 13:30:03 PDT
