[gmx-users] Size of perturbed groups in FEP

[Bruce Milne]

Hi everyone,

I have been wondering about the possibility of doing free energy 
calculations on D- and L- forms of amino acids incorporated into small 
peptides but I have no experience in this area and I was just wondering 
if it is possible to do free energy perturbations on groups as large as 
the side chains in e.g. isoleucine. It seems to me that changing a 
hydrogen atom for, say, a methyl group might be OK but what about 
something as large as -CH(CH3)CH2CH3 ?

I guess in practice the unit to be perturbed would have to include the 
backbone carbon plus the hydrogen and side chain in order to go from the 
D- to the L-form of an amino acid.

Sorry if this is really basic and obvious but any advice would be 
greatly appreciated.

Cheers,

Bruce

-- 
Dr. Bruce F. Milne PhD
CEQOFFUP
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
4050-047
Porto
Portugal

email: bfmilne at ff.up.pt
CEQOFFUP: http://www.ff.up.pt/ceqoffup/ceqoffup.html
Faculdade de Farmácia: http://sigarra.up.pt/ffup/web_page.inicial



	
	
		
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