As Anselm suggested, you will need to generate the prep file first.
Moving the two molecules into the proper relative alignment is not a
trivial thing to do. If you do not have an experimental structure or
a structure built some other way, then you will have to figure it out
yourself. As Anselm suggested, VMD or Chimera can help. You can also
use tleap commands to make geometric changes. Our group develops C++
source code because we frequently need to do very unusual things to
molecules.
What I'm trying to say is that this would be a challenge even for an
experienced person (*).
Do you know anything specific about the interactions? For example, do
you know which atoms are involved in hydrogen bonding between the two
strands? Do you know the proper orientation of the chains to each
other? Is there more than one orientation?
(*) I have been working with Nanome software in an Oculus Quest VR
headset recently. If you are looking for an easy way to move
molecules around based on chemical intuition, it does a nice job. It
can still take a little work to generate files useful for simulation.
The headset and the software will run you a little shy of $800 USD.
I've been using it to stick molecules in the various binding sites of
SARS-CoV-2. I believe the hardware can also be used to play games or
something.
On Mon, Apr 27, 2020 at 10:06 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
>
> Hi,
>
> just a quick answer and suggestion:
>
> > *Query 1: Regarding lignin:*
> >
> > But when I have tried according to your instructions, it says *could not
> > open the file: lignin.prep not found*. I have attached the screenshot
> > (li.png) of that.
> > I am using Amber 18 licensed version with Amber2019 Tools.
>
> >> You're going to need to generate a prep file for the molecule.
> >> Antechamber can do that. The manual explains reasonably well
>
> Have you successfully generated a prep file with parameters for your
> lignin system as suggested by Lachele? You have to to this first, before
> you can load the file into leap. The error message suggests that the
> prep file is "not found".
> Maybe you want to have a look into the manual, as recommended by Lachele.
>
> > *Query 2 : Regarding cellulose-hemicellulose chain: *
> >
> > To make the interaction between cellulose-hemicellulose chain, I need to
> > place them closer and parallel to each other.
> > [...]
> > However, I need to place
> > them close enough to see the hydrogen bonds between them. Similarly, I Need
> > to do this for cellulose bundles too. To do this what commands or procedure
> > I need to follow? Please let me know.
>
> If you want to build a structure from several parts, you could also use
> a graphical program like VMD or Chimera. In that, you can move the
> individual parts into their desired mututal position and save everything
> as total system. (Have a look at the manuals for how-to in detail.)
>
> Regards,
>
> Anselm
>
>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Apr 29 2020 - 18:30:02 PDT
