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
-- Regards Harmeet Kaur PhD Research Scholar Dr. Dinakar Salunke's Lab UNESCO Regional Centre for Biotechnology Biotech Science Cluster Faridabad, India. *Please do not print this e-mail unless otherwise required. Save paper, save trees.*
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