[gmx-users] transfer free energy

[Ilya Chorny]

Hi All I could really use some help on this simple formating issue.
Any help would be greatly appreciated.

I am attempting to calculate a transfer free energy but I needed to
create atoms  such as LJ1 and LJ2 and so on. I made the following
adjustments to ffoplsaanb.itp but when I run gromp I get an error
message.

Thanks

Ilya
 
On Mon, 2003-09-08 at 10:10, Ilya Chorny wrote:
> 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
> them.
>      Cu2+   Cu2+   63.546       2.000       A    2.08470e-01 
> 4.77295e+00
>      Fe2+   Fe2+   55.847       2.000       A    2.59400e-01 
> 5.44284e-02
>      Zn2+   Zn2+   65.370       2.000       A    1.95200e-01 
> 9.78874e-01
>        Ar   Ar     39.948       0.0         A    3.41000e-01 
> 2.74764e-02
>       LJ1   LJ1    39.948       0.0         A    2.41000e-01 
> 2.74764e-02
>       LJ2   LJ2    39.948       0.0         A    1.41000e-01 
> 2.74764e-02
>       LJ3   LJ3    39.948       0.0         A    0.41000e-01 
> 2.74764e-02
> 
> 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).
> > 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.