[gmx-users] transfer free energy

[Anton Feenstra]

Ilya Chorny wrote:
> Hello I am attempting to calculate the solvation free energy of Ar in
> H2O. I want to do an FEP calculation. For my first calulation of want to
> calculte the deltaA between Argon and LJ1 which I define as an at atom
> with a sigma 1 angstrom smaller then argon. I added LJ1 to
> ffoplsaanb.itp and to the .atp and .rtp files but when I run Grompp it
> tells me that it can not find LJ1. What am i doing wrong.

.atp and .rtp are used by pdb2gmx, not grompp. In stead, grommp reads all its
information from the included forcefield topologies, e.g. ffG43a1.itp, which in
turn includes ffG43a1bon.itp and ffG43a1nb.itp. Atomtypes are defined in the
ff*nb.itp file(s).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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