[gmx-users] error: Not enough ref_t and tau_t values!

[Yang Ye]

Prettina Anto_Louis wrote:

>Hello gromacs users!
>
>  Greetings!
>
>
>
>I was running simulation of a protein with a ligand.
>I have created  the topology for the ligand molecule
>with the help of PRODRG server and ran energy
>minimisation step successfully. But while I am running
>grompp before the mdrun program it is giving following
>error:
>Making dummy/rest group for T-Coupling containing 20
>elements
>Fatal error: Not enough ref_t and tau_t values!
>
>		Can you please tell me why I am getting such  an
>error? Also what are ref_t and tau_t values?
>  
>
You shall have set up the groups which cover all the atoms and assign 
ref_t and tau_t with each group.

>I encountered the following error after grompp:
>------------------------------------------
>processing coordinates...
>Shuffling coordinates...
>Entering shuffle_xv
>Sorting coordinates for     1 copies of molecule Protein_A
>Sorting coordinates for  9896 copies of molecule SOL
>Sorting coordinates for     0 copies of molecule K
>Sorting coordinates for     0 copies of molecule Na
>Sorting coordinates for     0 copies of molecule Ca
>Sorting coordinates for     0 copies of molecule Mg
>Sorting coordinates for     0 copies of molecule Cl
>Sorting coordinates for     0 copies of molecule Zn
>Sorting coordinates for     1 copies of molecule FRA
>Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW)
>Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW)
>Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW)
>Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW)
>Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW)
>Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW)
>Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1)
>Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2)
>  
>
There is a mis-alignment of the water molecule. The water in the spc.itp 
(or any other water) has the order of
1 OW
2 HW1
3 HW2
The order of the water molecule in your gro is
1 HW1
2 HW2
3 OW
you may have changed the order of atoms in spc.itp to get this pass.

>(more than 20 non-matching atom names)
>WARNING 2 [file "pla_drg.top", line 8006]:
>  14236 non-matching atom names
>  atom names from pla_drg.top will be used
>  atom names from after_em.gro will be ingnored
> 
>double-checking input for internal consistency...
>renumbering atomtypes...
>converting bonded parameters...
>#     ANGLES:   7484
>#      PDIHS:   3470
>#      IDIHS:   3180
>#       LJ14:   6948
>#     CONSTR:   3840
>#     SETTLE:   19792
>Walking down the molecule graph to make shake-blocks
>initialising group options...
>processing index file...
>Analysing residue names:
>Opening library file /opt/soft/gromacs/share/top/aminoacids.dat
>There are:  9898      OTHER residues
>There are:   123    PROTEIN residues
>There are:     0        DNA residues
>Analysing Protein...
>Analysing Other...
>Making dummy/rest group for T-Coupling containing 20 elements
>Fatal error: Not enough ref_t and tau_t values!
>
>-----------
>
>
>          thanking you!
>
>
>
>
>
>
>
>
>
>        "praise the lord!"
>
>
>With prayers,
>prettina
>
>
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