Re: [gmx-users] binding energy for membrane system

2013-07-25 Thread Justin Lemkul 



On 7/25/13 12:51 AM, Albert wrote:

Hello:

  I notice that the manual or tutorial in Gromacs (FEP, unbralla sampling, TI
and so on) website for binding energy evaluation are all for protein in water. I
am just wondering how can we evaluate the protein/ligand binding affinity for
membrane system accurately? Probably the most difficult thing is to evaluate the
term from protein/lipids and protein/water part, since the system is
heterogeneous instead of homogeneous.



Have a look through the literature to see what other people do.  The Gromacs 
manual and tutorials are not going to be definitive sources for everything, nor 
do they claim to be.  Probably PMF is the way to go.


-Justin

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==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] binding energy for membrane system

2013-07-24 Thread Albert 

Hello:

 I notice that the manual or tutorial in Gromacs (FEP, unbralla 
sampling, TI and so on) website for binding energy evaluation are all 
for protein in water. I am just wondering how can we evaluate the 
protein/ligand binding affinity for membrane system accurately? Probably 
the most difficult thing is to evaluate the term from protein/lipids and 
protein/water part, since the system is heterogeneous instead of 
homogeneous.


thank you very much.
Albert
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