On FASPR and rotamer sampling
Posted: Sun Jun 04, 2023 12:45 am
From: <l*@opnbnch.com>
Date: Friday, June 2, 2023 at 14:25
Subject: On FASPR and rotamer sampling
Hi Prof. Zhang,
I've been really impressed with using your FASPR tool - it's very fast and generates plausible coordinates. It's been a great addition to the suite of protein structure modeling tools out there at the moment - thank you for making it available!
I'm interested in generating ensembles of conformers with alternate rotamer states. One way to do this might be molecular dynamics / monte carlo, but I wondered if the FASPR tool can be hacked to do this. I looked in the code and found mention of a 'temp' variable, suggesting there's some kind of annealing going on. But the outputs are very consistent, suggesting that no sampling is occurring.
Do you know of a way to generate alternate conformers with FASPR? I'm happy to do a bit of hacking to implement it. Or alternatively, do you have a similar tool that might achieve the same end goal?
Thanks a lot,
Date: Friday, June 2, 2023 at 14:25
Subject: On FASPR and rotamer sampling
Hi Prof. Zhang,
I've been really impressed with using your FASPR tool - it's very fast and generates plausible coordinates. It's been a great addition to the suite of protein structure modeling tools out there at the moment - thank you for making it available!
I'm interested in generating ensembles of conformers with alternate rotamer states. One way to do this might be molecular dynamics / monte carlo, but I wondered if the FASPR tool can be hacked to do this. I looked in the code and found mention of a 'temp' variable, suggesting there's some kind of annealing going on. But the outputs are very consistent, suggesting that no sampling is occurring.
Do you know of a way to generate alternate conformers with FASPR? I'm happy to do a bit of hacking to implement it. Or alternatively, do you have a similar tool that might achieve the same end goal?
Thanks a lot,