On 1/9/17 2:31 AM, tasneem kausar wrote:
I got it.
I have looked at the input files for the T4-lysozyme tutorial available at
alchemistry.org. They have defined state A and state B. I am using
GROMACS-5.1.4 for these calculation. So as mentioned in gromacs manual
decoupling parameters are taken from the mdp options, like by defining
[lambda-moltype] in mdp file. As I know from the tutorials and manual the
solvation free energy of the ligand can calculated.
From the alchemistry.org input files, the topology parameters of ligand are
inserted in protein topology named as complex.top.
If I follow the same protocol without defining the state B of the ligand in
topology, how the ligand molecule will be decoulped in complex.
An explicit B-state is necessary for a relative free energy calculation, in
which one molecule is transformed into another.
For any absolute free energy calculation (solvation, binding, etc) then you do
not need to define a B-state, and just couple the physical parameters to lambda
to turn them on/off.
-Justin
On Sun, Jan 8, 2017 at 10:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/7/17 10:29 PM, tasneem kausar wrote:
Thank you for your reply
In last section of your tutorial you have suggested some changes to made
in
mdp file. That can be used for solvation free energies.
For free energy calculation of protein drug complex, is it only lambda
restraint to be defined?
Along with a complex system of [intermolecular_interactions] that preserve
the relative orientation of the ligand. This is a very complex calculation
in practice. See examples on alchemistry.org and in the literature in
works by Roux, Im, Karplus, etc. My tutorial is not very useful for such
calculations; it is extremely basic relative to what is needed to carry out
a binding free energy calculation. I only mentioned it there because so
many people asked about it and I wanted to clear up any confusion.
-Justin
On 8 Jan 2017 01:45, "Justin Lemkul" <jalem...@vt.edu> wrote:
On 1/7/17 6:05 AM, tasneem kausar wrote:
Dear all
I am following Justin's tutorial methane in water for free energy
calculation. I am using Gromacs-5.1.4. The charges of methane in
topology
are set to zero. So following the same protocol, is it relevant to set
the
charges at zero in topology of the drug. I am confused because in
tutorial
of Sander (ethanol in water) charges are present in the topology file.
Please tell me the difference in both the tutorials and how can I apply
it
to drug that I want to study.
The charges in my tutorial are set to zero because the stated goal of
that
tutorial is to reproduce *only the LJ portion of the hydration free
energy*
to match a published paper. This creates a very simple, robust system.
If
you want to calculate a real, meaningful hydration or binding free
energy,
charge transformation is required.
-Justin
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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