Hi there -
My typical workflow for free energy on membrane proteins with TI would be
* Equilibrate the system (receptor+single ligand) under NPT with semiisotropic barostat (ntp=3) for >100 ns
* Prepare/dock remaining ligand set using the equilibrated system
* Run TI windows using ntp=1. Although it would be preferable to keep ntp=3, this is not currently possible and since TI windows are typically short (on the order of 5 ns) you should not expect large changes in the membrane during these windows
If you run membrane proteins under ntp=1 for hundreds of nanoseconds, you may see the membrane contracting along either the X- or Y- axis (such that it thins in one dimension and expands in the other). This is the motivation for the semiisotropic barostat, but short 5-10 ns TI windows are unlikely to encounter this.
Best regards
Callum
-----Original Message-----
From: William Glass via AMBER <amber.ambermd.org>
Sent: Tuesday, May 7, 2024 6:06 AM
To: amber.ambermd.org
Subject: [AMBER] Alchemical membrane simulations with the AMBER TI code
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Hi,
I’d like to run alchemical membrane simulations with the AMBER TI code using the semiisotropic barostat (ntp=3). However, when I try to do this, I get an error:
ERROR: TI is incompatible with ntp != 0, 1
This seems to suggest that only isotropic barostat/no barostat is allowed, but there are some papers in the literature that seem to be running AMBER TI in NPT for membrane systems (e.g. see *J. Chem. Inf. Model.* 2021, 61, 12, 5923–5930). Are there any options or best practices for running alchemical membrane simulations with AMBER?
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Received on Tue May 07 2024 - 08:00:03 PDT
