Re: [AMBER] Multi-Monomer Polymer

From: Dr. Anselm Horn <>
Date: Fri, 25 Jun 2021 12:55:24 +0200


I had a quick look at the structures encoded in your prepi files
(converted them to pdb).
To me it seems that your systems comprise saturated compounds without
any open valences, which makes it impossible for tleap to generate a

The logic in using building blocks within tleap is that these blocks
collected in a library are in their ready-to-use structure, i.e.
mid-chain residues have two open valences, while terminal residues
posses only one. Thus, amino acids have three structural templates for
the biopolymer, N-terminal, mid-chain, C-terminal.

(You did not provide your leap *input*; maybe you already tried to
create terminal residue prepi files, and maybe the ycontain issues as well.)

Thus, have a closer yook at your prepi files.
For a first test, just load the mid-chain prepi files and try a
heterodimer system a = sequence { VAC HVC }.

Hope that helps.




On 06/24/2021 09:54 PM, Swisher, Justin S wrote:
> Hello, All
> Does Amber have the capability to build polymers composed of two non-standard units? I'm currently trying to build a polymer composed of polyvinyl acetate and polyvinyl caprolactam and when I use T-Leap to connect them the output file is giving me a chirality error based on faulty connection atoms. I started looking at the prepi files that I've generated to put them together because that seems to be where I can fix those connections, but when I go about editing the files so that they can match it is still giving me the same error where apparently Atom C2 from my VAC file does not match. I'm going to attach the three files I think are relevant, but perhaps I'm incorrect about them. The "hvcl_retry" is meant to be the head of the polymer and the middle is meant to be the "vace" file.
> Thank you for any help you can provide!
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Received on Fri Jun 25 2021 - 04:00:02 PDT
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