From: Jean-Patrick Francoia (jeanpatrick.francoia_at_gmail.com)
Date: Tue May 06 2014 - 13:38:43 CDT
Le 06/05/2014 20:06, Kenno Vanommeslaeghe a écrit :
> On 05/06/2014 03:35 AM, Jean-Patrick Francoia wrote:
>> "That said, your case sounds considerably simpler, so it will
>> probably be
>> easier for you to generate each branch as a linear chain of normal
>> CHARMM36 RESI LYS monomers, then graft the branches using a 2-residue
>> (which you need to put together yourself)."
>> I don't really understand the second part of your advice, but what
>> telling me is basically to minimize each branch normally, and then
>> assemble then, am I right ?
> No, the [psf] generation step precedes the assignment of Cartesian
> coordinates, which in turn precedes any energy calculation,
> minimization or simulation. During the generation step, you're working
> on the abstract graph that is the connectivity of the molecule, and it
> is during this step you can generate [the connectivity for] the linear
> segments and graft them together. After that's done, you have to worry
> about good "initial guess" Cartesian coordinates (for which I don't
> have much advice), and *only then* you can solvate, minimize and
> I always generate my psf using the CHARMM program, so I can give you
> detailed instruction on how to use that, but unfortunately, I'm not
> confident I can give you good advice for doing the same with psfgen or
>> Another thing I would like to ask is that if I can do what they
>> suggest in
>> the doc, for the glutathione (see joinded pdf, page 21). It seems a bit
>> hard for me but I can probably manage to do it. If I can't do it, I also
>> would like to know why (at least I would have learned something).
> This is one of the many possibilities I thought of before writing my
> last e-mail; it wouldn't work because glutathione is still linear,
> whereas you have a polymer hanging from both your main chain and your
> side chain. That's why I recommended you create a 2-residue patch
> instead. This isn't covered by that tutorial but it should give you
> the necessary background to understand the existing 2-residue patches
> in the CHARMM36 distribution and create your own by analogy. I'm not
> saying it will be easy to do for a novice, though.
>> I will not perform any energy calculations on it,
>> I will just use it with a small organic molecule to determine where it
> I fail to see how one can determine "where a molecule binds" without
> involving energetics of some sort.
"This is one of the many possibilities I thought of before writing my
last e-mail; it wouldn't work because glutathione is still linear,
whereas you have a polymer hanging from both your main chain and your
side chain. That's why I recommended you create a 2-residue patch
instead. This isn't covered by that tutorial but it should give you the
necessary background to understand the existing 2-residue patches in the
CHARMM36 distribution and create your own by analogy. I'm not saying it
will be easy to do for a novice, though. "
Why is it a problem a residue can bind on the 2 sides ? Isn't it
possible to modify the topology file to allow a bond on the main chain
and on the side chain ? I would like to, because I'm thinking about an
issue I could have with the other approach, if I understand it well.
Please correct me if I'm wrong, I'm trying to understand how the 2
residues approach works. You basically define a new residue, with a
length of n Lysines. Then you modify this residue on a certain amino
acid, to allow an epsilon bond. Then you create another residue, of a
length of m Lysines. Then you modify the last one to bond on the
carbonyl part. Am I right or not yet ?
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