[Chimera-users] How can I can calculate or know Gibbs free energy from UCSF Chimera

[Awah.Chidiebere.U at mh-hannover.de]

Dear Elaine C Meng,

Thanks for your warm response,


Best wishes


Chidi

-----Ursprüngliche Nachricht-----
Von: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Gesendet: Freitag, 28. August 2015 02:45
An: Awah, Chidiebere.U
Cc: chimera-users at cgl.ucsf.edu
Betreff: Re: [Chimera-users] How can I can calculate or know Gibbs free energy from UCSF Chimera

Dear Chidiebere U Awah,
(1) Sorry no, Chimera does not do free energy calculations.

(2) Sorry no, Chimera does not predict how macromolecules might bind one another.  Although you might think this is possible from molecular dynamics alone, typically the sampling space is so large that even extremely long simulations will not be useful, and additional programs such as docking may be needed.  Although the Chimera daily build does have a molecular dynamics simulation tool, this tool is still experimental.  It has limited options and is relatively slow (compared to other simulation programs), and there is no manual page for it yet.

The "MD Movie" tool in Chimera is not experimental, but it only shows the dynamics calculated by other simulation programs outside of Chimera (AMBER, Gromacs, etc.) as listed in the "startup and input" section here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

Some of those other programs are better choices for what you want to do, but I cannot advise you specifically which one(s) to use.  I recommend  reading scientific publications, textbooks, online information, etc. for more information.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

P.S. for Chimera questions, this is the proper address (chimera-users at cgl.ucsf.edu)

On Aug 27, 2015, at 7:43 AM, <Awah.Chidiebere.U at mh-hannover.de> <Awah.Chidiebere.U at mh-hannover.de> wrote:

> Dear Colleagues,
> Thanks for developing such wonderful tools as Chimera for molecular dynamics analysis of structure.
> Please I have two questions:
>  
> 1.       Is it possible to calculate Gibbs free energy  from complexes on UCSF Chimera,  for examples when  complexes are solvated?
> 2.       On building structures , is it possible to simulate how a given complex could bind DNA oligos , for example  when one makes  changes in single nucleotides and ask  a given  DNA binding TF structure to bind it on Chimera?
>  
> I would look forward to your response to these questions. I would also be very happy if I could speak by phone with the administrators.
>  
> Thanks. 
> Best wishes,
>  
> Chidiebere U Awah MD Msc
> PhD student , Molecular Medicine
> Hannover Medical School , Germany.