[gmx-users] Free energy and pdb2gmx

[Anton Feenstra]

carmien at alumni.uv.es wrote:
> Since I can calculate the solvatione free energy using thermodinamic
> integration or perturbation, does anybody know which method provides
> more accurately results?? (I don't have experimental data for the
> different size boxes...)

You'll need to have a path from one solute to the other to use TI or FEP.
I.e. they must have similar topologies so what are atoms in one molecule
can become dummies (mass, but no interactions) in the other molecule.
FEP works if differences are small, so can be regarded as 'perturbation'
and /can/ be more accurate if this assumption holds well.

> This second question is only related with D and L-arginine. I downloaded
> several .pdb files in order to create the top and .gro files. My problem
> appears when I execute the following command line:
> 
>                               pdb2gmx  -f  D(or L)-arginine.pdb

IIRC, pdb2gmx does not work with single-residue chains. Something to do
with tagging the same residue as C- and N-terminus at the same time.
Have you tried this with other residues as well?

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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