[gmx-users] Size of perturbed groups in FEP

Bruce Milne bfmilne at ff.up.pt
Wed Jan 11 15:24:29 CET 2006

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.



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

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

Yahoo! Messenger - NEW crystal clear PC to PC calling worldwide with voicemail http://uk.messenger.yahoo.com

More information about the gromacs.org_gmx-users mailing list