[gmx-users] Error: 1 atoms are not part of any of the T-Coupling groups

[Justin A. Lemkul]

On 5/3/12 12:32 PM, kalai arasan wrote:
> Dear,
>           I am working in complex protein which contains one ligand and one Mg2+
> ion. I am got an error while running grompp for NVT.
>
> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
>
> ---------------------------------------------------------------------------------------
> Program grompp, VERSION 4.5.3
> Source code file: readir.c, line: 1402
>
> Ftal error:
> 1 atoms are not part of any of the T-Coupling groups
> ------------------------------------------------------------------------------------------
>
> For creating the index file before grompp i used the following command
>
> make_ndx -f em.gro -o index.ndx
>
>    0 System              : 248986 atoms
>    1 Protein             :  5019 atoms
>    2 Protein-H           :  3975 atoms
>    3 C-alpha             :   519 atoms
>    4 Backbone            :  1557 atoms
>    5 MainChain           :  2077 atoms
>    6 MainChain+Cb        :  2556 atoms
>    7 MainChain+H         :  2575 atoms
>    8 SideChain           :  2444 atoms
>    9 SideChain-H         :  1898 atoms
>   10 Prot-Masses         :  5019 atoms
>   11 non-Protein         : 243967 atoms
>   12 Other               :    24 atoms
>   13 MG2+                :     1 atoms
>   14 UNK                 :    23 atoms
>   15 NA                  :     1 atoms
>   16 Water               : 243942 atoms
>   17 SOL                 : 243942 atoms
>   18 non-Water           :  5044 atoms
>   19 Ion                 :     1 atoms
>   20 MG2+                :     1 atoms
>   21 UNK                 :    23 atoms
>   22 NA                  :     1 atoms
>   23 Water_and_ions      : 243943 atoms
>
>   nr : group       ! 'name' nr name 'splitch' nr    Enter: list groups
> 'a': atom & 'del' nr 'splitres' nr 'l': list residues
> 't': atom type   | 'keep' nr 'splitat' nr 'h': help
> 'r': residue 'res' nr 'chain' char
> "name": group 'case': case sensitive 'q': save and quit
> 'ri': residue index
>
>  > 1 | 14
>
> Copied index group 1 'Protein'
> Copied index group 14 'UNK'
> Merged two groups with OR: 5019 23 -> 5042
>
>   24 Protein_UNK         :  5042 atoms
>
>  > q
>
>
> nvt.mdp i used
>
> title       = Protein-ligand complex NVT equilibration
> define      = -DPOSRES
> integrator  = md
> nsteps      = 50000
> dt          = 0.002
> nstxout     = 100
> nstvout     = 100
> nstenergy   = 100
> nstlog      = 100
> energygrps  = Protein UNK
> continuation    = no
> constraint_algorithm = lincs
> constraints     = all-bonds
> lincs_iter      = 1
> lincs_order     = 4
> ns_type     = grid
> nstlist     = 5
> rlist       = 0.9
> rcoulomb    = 0.9
> rvdw        = 1.4
> coulombtype     = PME
> pme_order       = 4
> fourierspacing  = 0.16
> tcoupl      = V-rescale
> tc-grps     = Protein_UNK Water_and_ions
> tau_t       = 0.1   0.1
> ref_t       = 300   300
> pcoupl      = no
> pbc         = xyz
> DispCorr    = EnerPres
> ; Velocity generation
> gen_vel     = yes
> gen_temp    = 300
> gen_seed    = -1
>
> I am not clear how i can add MG2+ while creating index.ndx file. Please help me
> out.
>

Three approaches:

1. Create a group that replaces "Water_and_ions" with one that contains the MG2+ 
ion within the solvent
2. Add MG2+ to residuetypes.dat so that it is recognized as an ion
3. Couple the MG2+ and protein/ligand together, as might make the most physical 
sense

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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