RE: Amber topology for mutation

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Sep 16 2019 - 13:22:25 CDT

It still works, but the setup is totally different. For mutation, you need a system that has both the original residue and the new residue in the structure. Once you get to that stage, its *relatively* straightforward, since then the usual pdb tagging tricks will still work, but the NAMD tutorial and the special patches all assume a CHARMM-style psf, and I'm not familiar enough with Amber to know if there is an equivalent.

-Josh

On 2019-09-16 11:47:40-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

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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