On 11/9/13 12:48 AM, pratibha wrote:
Sorry for the previous mistake. Instead of 53a7, the force field which I
used was 53a6.
53A6 is known to under-stabilize helices, so if a helix did not appear in a
simulation using this force field, it is not definitive proof that the structure
does not populate helical structures. I generally see mixed opinions in the
literature in terms of which Gromos parameter set is the most reliable. As was
asked by someone else, is there a reason you are only considering Gromos
parameter sets? Others may be better suited to your study.
-Justin
On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012325...@n6.nabble.com> wrote:
On 11/7/13 12:14 PM, pratibha wrote:
My protein contains metal ions which are parameterized only in gromos
force
field. Since I am a newbie to MD simulations, it would be difficult for
me
to parameterize those myself.
Can you please guide me as per my previous mail which out of the two
simulations should I consider more reliable-43a1 or 53a7?
AFAIK, there is no such thing as 53A7, and your original message was full
of
similar typos, making it nearly impossible to figure out what you were
actually
doing. Can you indicate the actual force field(s) that you have been
using in
case someone has any ideas? The difference between 53A6 and 54A7 should
be
quite pronounced, in my experience, thus any guesses as to what "53A7"
should be
doing are not productive because I don't know what that is.
-Justin
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