Re: [AMBER] styrene sulfonate molecule building using xleap

From: David A Case <>
Date: Wed, 24 Apr 2019 07:45:08 -0400

On Wed, Apr 24, 2019, Shilpa Gupta wrote:

>I am trying to model poly (sodium styrenesulfonate) using xleap. For this
>first i have tried to build the single unit of styrene sulfonate but after
>running antechamber an error is coming which i am providing here

Antechamber only works on complete molecules, not on fragments or
"monomers" of polymers.

>*Welcome to antechamber 17.3: molecular input file processor.Info: Total
>number of electrons: 89; net charge: -1Info: The number of electrons is odd

Another way of saying this is that you need to give sqm a closed shell
system. Generally, you would need to "cap" the monomer with blocking
groups, then remove them later. This is similar to looking at a
"modified residue" for biopolymers.

cc-ing to Junmei, since I think he had promised to make the workflow for
doing this sort of analysis easier. See this tutorial to get started:


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Received on Wed Apr 24 2019 - 05:00:03 PDT
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