[gmx-users] Pull code grompp error

Souparno Adhikary souparnoa91 at gmail.com
Fri Mar 24 07:48:29 CET 2017


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.


Souparno Adhikary
University of Calcutta,

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