[gmx-users] transfer free energy

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Mon Sep 8 19:11:02 CEST 2003

I added the atomtype to ffoplsaanb.itp as follows:

; These ion atomtypes are NOT part of OPLS, but since they are
; needed for some proteins or tutorial Argon simulations we have added
     Cu2+   Cu2+   63.546       2.000       A    2.08470e-01 
     Fe2+   Fe2+   55.847       2.000       A    2.59400e-01 
     Zn2+   Zn2+   65.370       2.000       A    1.95200e-01 
       Ar   Ar     39.948       0.0         A    3.41000e-01 
      LJ1   LJ1    39.948       0.0         A    2.41000e-01 
      LJ2   LJ2    39.948       0.0         A    1.41000e-01 
      LJ3   LJ3    39.948       0.0         A    0.41000e-01 

But when I try to run Grompp on my topology it gives me the following
error message:

Fatal error: Atomtype 'LJ1' not found!

My topology file has the line

#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass 
typeB    chargeB      massB
     1         Ar      1     AR     AR      1          0     39.948
LJ1        0           39.948

On Sun, 2003-09-07 at 22:56, Anton Feenstra wrote:
> 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).

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