Hi, S. Bill,
The mbondi (and mbondi2) variables are usually only pertinent when using GB,
as they define the various intrinsic radii used by GB. The new version of
AMBER - AMBER11 - will have new intrinsic radii, parametrized using massive
training sets. To answer your question, the quality of PB comes from
calculating the intrinsic radii, so mbondi and mbondi ought not affect the
results too much. However, it is common practice to always specify mbondi2,
even if you're using TIP3P. Unless you want mbondi instead of mbondi2 - say
previous work on your proposed work has shown better results, however
unlikely - then go with it. But otherwise, specify mbondi2, even when using
PB.
Hope this helps,
kevin
On Sun, Mar 21, 2010 at 3:55 PM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> Dear AMBERUsing mbondi or mbondi2 affects MD simulation? In other words,
> the resulted MD trajectories will be different in case I used mbondi instead
> of mbondi2.Or it just makes sense during MM-PBSA calculation?Thanks in
> advanceS. bill
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-- - -
HK
-------------------------------------------------------
Kevin Eduard Hauser
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
(631) 913.3194
(561) 635.1848
84hauser.gmail.com
-------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 21 2010 - 14:00:03 PDT
