Steered molecular dynamics simulations of peptide with non standard amino acid using GAFF parameter

From: Nicholus Bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Sat Feb 05 2022 - 03:30:16 CST

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Hello everyone,

This is the third time I am putting up this question without any answer.
Kindly let me know any possible explanation.

I have a 20 mer homopeptide with a non standard amino acid. I am using GAFF
parameter to simulate it. I could run 1 microsecond simulations of this
peptide without any problem. The peptide is of helical confirmation.

However, I am facing problem running SMD unfolding of the peptide. Even
with a velocity of .25 angstrom per nano second and force 4kcal/mol the
peptide is unfolding too quickly i. e. end to end distance going from
around 25 to 100 angstrom within 100 pico second and the peptide become
fully streched.

Can anyone kindly guide on this. Is GFFF parameter not suitable for running
SMD unfolding.

Thank you in advance

Regards

• Next message: İmren Bayıl: "Unable to open binary file md_equ_300.out.rst.vel"
• Previous message: Francesco Pietra: "Re: No xyz and scfp files in QMMM ORCA output"
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