[gmx-users] transfer free energy
ichorny at maxwell.compbio.ucsf.edu
Tue Sep 9 20:03:01 CEST 2003
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
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
> 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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