[gmx-users] Size of perturbed groups in FEP

Maik Goette mgoette at mpi-bpc.mpg.de
Wed Jan 11 16:33:39 CET 2006


I think its practicable. You should use softcore potential in that case.

I don't think, that you have to include the BB-atoms, too.
You can do that, but I can't see the need for that.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Bruce Milne wrote:
> 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

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