[gmx-users] Pull code grompp error

[Tasneem Kausar]

Define you pull group in index file  as the error message says.

On Fri, Mar 24, 2017 at 12:18 PM, Souparno Adhikary <souparnoa91 at gmail.com>
wrote:

> Hi,
>
> Below is my .mdp code for pulling as found in the tutorial by Justin
> Lemkul. I made the required changes to match my version syntax.
>
> pull                    = umbrella
> pull_ngroups            = 2
> pull_group0        = Protein_chain_A
> pull_group1        = DNA_chain_B
> pull_group2        = DNA_chain_C
> pull_geometry    = distance      ; simple distance increase
> pull_dim         = Y N N
> pull_rate1        = 0.01          ; 0.01 nm per ps = 10 nm per ns
> pull_rate2        = 0.01
> pull_k1           = 1000          ; kJ mol^-1 nm^-2
> pull_k2           = 1000
> pull_start       = yes           ; define initial COM distance > 0
>
> When I tried to grompp using this code, it generates an error:
>
> Fatal error:
> Group topol_Protein_chain_A referenced in the .mdp file was not found in
> the 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.
>
> I searched for the solutions in the Gromacs forum and found it might be due
> to name mismatch. But, in my case, the names are exactly same as referenced
> in the *.mdp file. Below is the molecule names from the topol.top file.
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> DNA_chain_B         1
> DNA_chain_C         1
> SOL         33542
> NA               125
> CL               98
>
> Can you please help to solve the problem? I tried with changing the names
> to Protein and DNA (the residue types) and changing the ngroups to 3.
> Nothing worked.
>
> Regards,
>
> Souparno Adhikary
> University of Calcutta,
> India.
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