[AMBER] Fwd: Failed TI heating simulation (RBFE) using Amber22

From: Pengfei Li via AMBER <amber.ambermd.org>
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´╝î

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]
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image.png
(image/png attachment: image.png)

CodeSnippet_TI.png
(image/png attachment: CodeSnippet_TI.png)

heating.0.out.png
(image/png attachment: heating.0.out.png)

heating.1.out.png
(image/png attachment: heating.1.out.png)

heating.log.png
(image/png attachment: heating.log.png)

Received on Sun Sep 04 2022 - 19:30:02 PDT
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