[gmx-users] Pull code grompp error
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:
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
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
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.
University of Calcutta,
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