From: Stefan Lyne Oliver (
Date: Tue Nov 01 2022 - 22:09:45 CDT

Hi All,

I've been working through the simple MDFF tutorial. Unfortunately, after completing the NAMD (2.14 for Win64-multicore-CUDA) simulations the 1ake does not fit into the map. There is evidence that the molecular dynamics is working as I can see movement of the 1ake model after I've performed the NAMD simulation. I've tried this on two different windows machines (VMD 1.9.4a53) with reproducible results. The provided ake-step1-result.dcd and ake-step2-result.dcd files work fine when I load the molecules so I must be missing something in the tutorial. I've spent a fair amount of time on this and also discovered what seem to be some errors in the commands e.g. it looks like in the 'Defining secondary structure restraints' section the 1ake-initial_autopsf.psf file in step 2 should be 1ake-initial-docked_autopsf.psf. Correcting either way produces the same results. Can you please let me know what I'm missing in the tutorial so that I can be confident in using the procedure on my own maps and models. Thanks in advance.

Best wishes,


Stefan Oliver, Ph.D.<;!!DZ3fjg!51MYNyLiezctxPXHZe7Rr6C1JinXT1yMsUFfvMrzwC4aAKakwizzvu08FacpuuIg9MdrXza3qFCXslwQLDzAqew$ >
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