Hi, this came up recently on the mailing list. Here was my response-
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,
Callum
-----Original Message-----
From: 변진영 / 학생 / 약학과 via AMBER <amber.ambermd.org>
Sent: Monday, June 17, 2024 6:11 AM
To: amber.ambermd.org
Subject: [AMBER] Using ntp=1 for membrane embedded Protein-Ligand System with ifsc=1 Option
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Dear AMBER Community,
I am currently working on a simulation involving a membrane-embedded protein-ligand system. Typically, for such systems, I used the following
settings:
- barostat = 2
- ntp = 3
- csurften = 3
- gamma_ten = 0.0
- ninterface = 2
However, I have encountered an issue when trying to calculate the relative binding free energy of the protein-ligand system using the '*ifsc*' option.
The 'ifsc' option only supports ntp=1, which conflicts with my usual settings for membrane-embedded systems.
Given this constraint, I am seeking advice on whether it is acceptable to run the simulation with ntp=1 for a membrane-embedded protein-ligand system.
Are there any potential issues or considerations I should be aware of when using this setting?
Any insights or recommendations from those with experience in similar simulations would be greatly appreciated.
Thank you for your assistance.
Best regards,
Jinyoung
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Received on Mon Jun 17 2024 - 09:00:02 PDT
