we have published many examples of 2D umbrella sampling in Amber.
for example, see the Methods sections in these articles:
Rational modulation of the induced-fit conformational change for slow-onset
inhibition in M. tuberculosis InhA
Lai, C-T., Li, H; Yu, W., Shah, S., Bommineni, G., Perrone, V.,
Garcia-Diaz, M., Tonge, P., Simmerling, C., Biochemistry, 2015, 54 (30),
4683-4691
DOI: 10.1021/acs.biochem.5b00284
A structural and energetic model for the slow-onset inhibition of the
Mycobacterium tuberculosis enoyl-ACP reductase InhA
Li, H.; Lai, C.; Pan, P.; Yu, W.; Liu, N.; Bommineni, G.; Garcia-Diaz, M.;
Simmerling, C. .; Tonge, PJ., ACS Chemical Biology, 2014, 9, (4), 986–993
DOI: 110.1021/cb400896g
Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase
Bergonzo, C., Campbell, A., de los Santos, C., Grollman, A and Simmerling,
C., Journal of the American Chemical Society, 2011, 133, 14504–14506
DOI: 10.1021/ja205142d
On Wed, Jun 8, 2016 at 12:16 AM, Airy Sanjeev <airy.sanjeev01.gmail.com>
wrote:
> Dear Amber Users,
> I wanted to do umbrella sampling with two degrees of freedom for a
> dimer system. How to proceed?
> One being the distance between the monomeric units in the dimer and
> the other one is angle along the axes between the monomeric units.
>
> Thanks in advance
>
> --
> with best regards,
> Airy Sanjeev
> Research Scholar
> Dept. of MBBT
> Tezpur University
> Napaam,Tezpur-784028
> Sonitpur,Assam
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 08 2016 - 04:30:02 PDT
