[AMBER] Imaging and connectivity error

From: Harmeet Kaur <meet.academia.gmail.com>
Date: Thu, 13 Aug 2015 16:57:24 +0530

Dear Amber Users

My system is a receptor of 2 subunits bound with 8mer peptide, simulated
for 1micro-sec using iwrap=1. I've used various combinations of 'image' and
'unwrap' to center the molecule, but the sub-units tend to diffuse out. My
last attempt was using 'autoimage origin'. Although the molecule is now
centered, it shows some connectivity issues (a snapshot attached for
reference). Can I proceed with it for further analyses? If not, please
suggest how to troubleshoot the same.
The script used was:

trajin prod_1kcs.mdcrd
strip :WAT
strip :Na+
strip :Cl-
autoimage origin
trajout 1kcs-autoimage_dry.mdcrd nobox

Harmeet Kaur
PhD Research Scholar
Dr. Dinakar Salunke's Lab
UNESCO Regional Centre for Biotechnology
Biotech Science Cluster
Faridabad, India.
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Received on Thu Aug 13 2015 - 04:30:05 PDT
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