[gmx-users] TFE

Emran Heshmati heshmaty at yahoo.com
Thu Aug 13 10:40:37 CEST 2015

 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. 

Best Regards
Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist
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