[AMBER] Setting custom parameters for CpHMD simulations

From: Jade Shi <jadejshi.hotmail.com>
Date: Wed, 10 Jun 2020 22:38:59 +0000

Hi all,
New user of AMBER here. I'm running CpHMD simulations on some proteins containing cysteines, and I'd like to implement the parameters described in the following paper: Liu et al., J. Am. Chem. Soc. 2019, 141, 6553-6560.

Specifically, the relevant section in methods:

The GB-based continuous CpHMD22 simulations were performed using the pmemd program in Amber18.48 Proteins were represented by the ff14SB force field,30 and solvent was represented by the GB-Neck2 implicit-solvent model49 with mbondi3 intrinsic Born radii and 0.15 M ionic strength. Note that cysteine parameters were not set in the GB-Neck2 model.49 Following the guidelines given in the GB-Neck2 paper49 and test calculations of the solvation free energy of the blocked cysteine model compound (with the N terminus acetylated and the C terminus amidated), we set the scaling parameter (Sx) of sulfur to that of oxygen (1.061039) and increased the intrinsic Born radius from the default value of 1.8 to 2.0 .

I was able to set up everything except the bolded section, where the authors modify two sulfur parameters, the scaling parameter and the intrinsic Born radius. Could someone please tell me the program/commands to do this?

Thanks a lot!
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Received on Wed Jun 10 2020 - 16:00:05 PDT
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