[gmx-users] nvt equilibration

[marzieh dehghan]

Hi

thank you for your answer

I used the following instructions: make_ndx -f em.gro -o index.ndx

and appear thses text:

Reading structure file
Going to read 0 old index file(s)

Analysing residue names:
There are:   421      Other residues
There are:  4446      Water residues
There are:    10        Ion residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

  0 System              : 13871 atoms
  1 Other               :   523 atoms
  2 UNK                 :   523 atoms
  3 CL                  :    10 atoms
  4 Water               : 13338 atoms
  5 SOL                 : 13338 atoms
  6 non-Water           :   533 atoms
  7 Ion                 :    10 atoms
  8 UNK                 :   523 atoms
  9 CL                  :    10 atoms
 10 Water_and_ions      : 13348 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

-- 
so, I selected

> 4 | 9
> 2 | 8


since in my em.gro file, protein and ligand called UNK, I dont know how to
select them as a group????


------ after that I hold thses command:
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

I confronted to the following error:

Group CL_Water not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the '-n' option of grompp.



please let me know, how can I solve this problem?????

thanks a lot








*Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
Biophysics (IBB)University of Tehran, Tehran- Iran.*