[AMBER] Multi-Monomer Polymer

From: Swisher, Justin S <Swisher122.live.missouristate.edu>
Date: Thu, 24 Jun 2021 19:54:04 +0000

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!

AMBER mailing list

Received on Thu Jun 24 2021 - 13:00:02 PDT
Custom Search