[AMBER] styrene sulfonate molecule building using xleap

From: Shilpa Gupta <guptashilpa0605.gmail.com>
Date: Wed, 24 Apr 2019 12:02:36 +0530

Dear Amber Users,
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* input *is:
*antechamber -j 5 -at sybyl -dr no -i pas.pdb -fi pdb -o pas.mol2 -fo mol2
-c bcc -nc -1*

and *output* is

*Welcome to antechamber 17.3: molecular input file processor.Info: Total
number of electrons: 89; net charge: -1Info: The number of electrons is odd
(89). Please check the total charge (-nc flag) and spin multiplicity
(-m flag).Running: /home/shilpa/Desktop/amber/amber18/bin/sqm -O -i sqm.in
<http://sqm.in> -o
Fatal Error!Cannot properly run "/home/shilpa/Desktop/amber/amber18/bin/sqm
-O -i sqm.in <http://sqm.in> -o sqm.out"*
will it be possible to build this sort of molecule and then further linear
polymer. If any one has any other method to
build this molecule their suggestion will be highly helpful for me. Thanks
in advance.

Shilpa Gupta
University of Delhi
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Received on Wed Apr 24 2019 - 00:00:02 PDT
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