[gmx-users] TFE

Justin Lemkul jalemkul at vt.edu
Thu Aug 13 13:57:27 CEST 2015

On 8/13/15 4:37 AM, Emran Heshmati wrote:
>   Dear Gromacsians
> I want to simulate a protein (MAJOR PRION PROTEIN) structure in TFE (trifluoroethanol) instead of water. I followed these steps:
> 1- I build tfe.pdb and tfe.itp using ATb server, (gromos force field: G54A7FF)
> 2- I placed tfe.itp file in directories: /usr/share/gromacs/top and  /usr/share/gromacs/top/gromos54a7.ff
> 3- I build tfe.gro from tfe.pdb using editconf command (editconf -f tfe.pdb -o tfe.gro) and placed it in the working directory.
> 4- I followed jastin lemkul recommended procedure ((lysozyme in water)):
>   pdb2gmx -f 4HE7.pdb -o 4HE7_processed.gro
>   editconf -f 4HE7_processed.gro -o 4HE7_newbox.gro -c -d 0.75 -bt dodecahedron
>   genbox -cp 4HE7_newbox.gro -cs tfe.gro -o 4HE7_solv.gro -p topol.top
> but the latest step (genbox command) takes too long and remains unfinished. this is what I see in the terminal:
> Reading solute configurationMAJOR PRION PROTEINContaining 159 atoms in 16 residuesInitialising van der waals distances...
> WARNING: Masses and atomic (Van der Waals) radii will be guessedbased on residue and atom names, since they could not bedefinitively assigned from the information in your inputfiles. These guessed numbers might deviate from the massand radius of the atom type. Please check the outputfiles if necessary.
> Reading solvent configuration"ALL ATOM STRUCTURE FOR MOLECULE UNK"solvent configuration contains 9 atoms in 1 residues
> what is wrong? help me please.

"solvent configuration contains 9 atoms in 1 residues"

genbox expects -cs to be a *box* of solvent, not a single residue.

Note that 9 atoms implies an all-atom model of TFE, which is probably 
incompatible with the united-atom GROMOS force field.  You might be able to 
download an all-atom coordinate file, but the topology likely has a UA 
representation of C1.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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