Date: Mon, 5 Sep 2022 09:59:56 +0800
Dear all,
When we performed one relative binding free energy simulation using
Amber22, one error log (please see attached heating.log.png) occurred.
Then, we checked the md output files (heating.0.out.png &
heating.1.out.png), and we found that there is a wired issue where VDW
energy appears to be too large, although both ligands have been aligned
well for their linear atoms. We also used the same md input files to do the
same simulations using Amber20, then everything worked well.
We found that it should be caused by missing one loop for linear atoms' xyz
coordinates copy from TI region 1 to TI region 2 as seen from line 970 of
ti.F90 file (CodeSnippet_TI.png) of Amber22. After we fixed this point,
everything also can work well now.
Please take a look at this issue here. Thanks!
Best regards，
Pengfei Li
----------------------------------------
Senior Application Scientist at
Single Particle, LLC
pengfei.li.singleparticle.com
https://www.singleparticle.com <http://singleparticle.cn/>
https://twitter.com/singleparticle
Single Particle, your one-stop shop for structural biology needs
[image: image.png]
STATEMENT OF CONFIDENTIALITY: The information contained in this electronic
message and any attachments to this message are intended for the exclusive
use of the addressee(s) and may contain confidential or privileged
information. Legal privilege may apply and is not waived for unintended
recipients. Any unauthorized review, use, disclosure or distribution is
prohibited. If you are not the intended recipient, please notify the sender
as soon as possible, and destroy all copies of this message and any
attachments whether stored electronically, physically, or otherwise. Please
be advised that the content of this message is subject to access, review
and disclosure by the sender's email system administrator. Single Particle
LLC accepts no liability for any damage caused by any virus or malware
transmitted by this email.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/png attachment: image.png)
(image/png attachment: CodeSnippet_TI.png)
(image/png attachment: heating.0.out.png)
(image/png attachment: heating.1.out.png)
(image/png attachment: heating.log.png)
