[AMBER] Free energy calculation: Thermodynamic integration with use of restraints

From: <vladimir.palivec.marge.uochb.cas.cz>
Date: Wed, 25 Mar 2015 18:55:45 +0100


this question is similar to this one:


however, I think I quite did not get it.

I would like to do a thermodynamic integration simulations to calculate dG
of binding of a ligand to a protein. After search through a literature I
decided to do it in multiple steps:

1. constrain a ligand in a certain position using 6 restraints
 - here i need to calculate dG of proposing restraints

2. turn off el. i.

3. using soft core, turn off vww interactions

4. analytically remove restraints

I am not sure how to perform the step 1. I thought it is possible to use
pmemd with single topology and gradually propose restraints and thus get
the dG (with use of nmropt=1 and DIANG file). However, I have no found any
way to do it - either in manual or forum. Please, can somebody give me a
hint how this calculation should be performed? How to set up the
calculation and how to obtain energy of proposing restraints?

Is it even possible to do it with one topology file?

Thank you very much for any help!


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Received on Wed Mar 25 2015 - 11:00:03 PDT
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