Re: Amber topology for mutation

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Mon Sep 16 2019 - 12:42:12 CDT

What do you mean? The methodology have to be force field independent. Why would alchemical FEP not work if you use another force field?

On Mon, Sep 16, 2019 at 11:44 AM Aashish Bhatt <aashish.ph16221_at_inst.ac.in<mailto:aashish.ph16221_at_inst.ac.in>> wrote:
Dear Sir

I have followed the tutorial "A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD" section 3 :Mutation of tyrosine into alanine"
I have trying to calculate free energy perturbation for mutating protein.
My main problem is i am using amber topology.
Is there any alternative for this methodology to be used in amber format?

Best Regards
Aashish



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