Hi
Note that since this tutorial part for explanation of parts of an MM-PBSA
calculation.
As I understand it to be see the structures you want are two separate files
ligand (substrate / inhibitor) and the protein.
This u can in the early stages of preparing the PDB files for Simulations
Amber
Take a look at the initial preparation of the systems in the manul of amber
using the program pdb4amber vc will start treating your sitema generating
several files to run the program.
The end of his execusão list up in the terminal window an information
sequence. I suggest you save these in a file to see also later (I even
think this should already
be automatic camo creation other files).
In the waste will not be standard crystallographic information about
binders, metals (if applicable), or parts of your system you will have to
have greater attention.
In short what do you prescisa is to locate its ligand salver pdb it. And to
take your protein from your file coordinates.
If a non-standard residue using pdb4amber this will be done.
Regards,
Marcelo
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2016-02-28 4:39 GMT-03:00 Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>:
> Hi,
> Excuse me, I have a real basic question. I am going through the tutorial 3.
>
> http://ambermd.org/tutorials/advanced/tutorial3/section1.htm
>
> and I do not know how could I prepare ras.pdb and raf.pdb from the
> ras-raf.pdb complex?
>
> I really appreciate if you could help me,
> Bests
> Mahdieh
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Received on Sun Feb 28 2016 - 04:30:03 PST
