Re: [AMBER] Interaction of cellulose-hemicellulose

From: Dr. Anselm Horn <>
Date: Mon, 27 Apr 2020 16:04:57 +0200


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.)



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Received on Mon Apr 27 2020 - 07:30:02 PDT
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