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

[kalai arasan]

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.


P.Kalaiarasan
National Centre of Applied Human Genetics
School of Life Sciences
JNU
New Delhi
India
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