[gmx-users] mutation FE calculation with oplsaa

Maik Goette mgoette at mpi-bpc.mpg.de
Mon Jun 2 16:40:26 CEST 2008


1. Yes, you have to define both A and B parameters. As far as I 
understand, GROMPP can't know, that the first parameters it finds are 
those of the B-state, not the A-state.
The parameters are directly taken from the FF files for the atom 
pairs,triple and quartetts.


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/

Qiang Li wrote:
> Dear all users,
> 1,
> I am modifying the .top file for mutation free energy calculation(A->B), 
> so I need the provide the parameters of structure A and B in [bonds], 
> [angles], [dihedrals].
> Is it possible for me to provide only the parameters of B but le 
> the grompp using the default parametes of initial structure A? 
> I know the A parameters will be copied to B if parameters of B is not 
> explicitly defined in .top. IS that means I must explicitly define both 
> A and B at the same time?
> I ask it since I find in OPLSAA force field the .top file does not 
> contain paramters of [bonds], [angles],... but only the atome numbers 
> and function types. 
> 2,
> When comparing the solvation free energy tutorial from 
> http://md.chem.rug.nl <http://md.chem.rug.nl/> and the wiki(Dillgroup), 
> I get confused at the definition of solvation free energy.
> In the former, dG=dG1(in vacuo)-dG2(in water); however, in the latter it 
> seems only calculating the dG2(in water) gives excellent result compared 
> to expt.
> Did I misunderstand anything here?
> thanks a lot
> LQin 
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