[gmx-users] Insertion protein in the membrane via G_membed

James Starlight jmsstarlight at gmail.com
Wed Jun 20 10:40:30 CEST 2012

But where exactly error in such inclussion ?

In G_membed manual I've found only this statement about inclussion of the

    When the group to embed is not a default group, such as a protein and
its crystal water, an ndx file
should also be provided to g membed. Make sure all the molecule types in
the group to embed are unique,
e.g. the molecule type of the crystal waters should be different from that
of the solvent. Also the freeze
and energy exclusion parameters in the mdp file should be changed to match
the name of the group to

This tell nothing how exactly define mdp file. The way that I've used gave
me those strange error that pop ( membrane ) was in the first group wich
really contained of only merged protein and ligand (2 different mol.
types). This merging I've done by means of index_ndx based on the GRO file
with I've provide to GROMPP.

Also I've tried to do it in another manner defining all groups separately

integrator     = md
energygrps      = Protein ADN
freezegrps     = Protein ADN
freezedim      = Y Y Y Y Y Y
energygrp_excl = Protein Protein

In that case I have no such problem but during insertion G_membed has
deleted ADN.


2012/6/20 Mark Abraham <Mark.Abraham at anu.edu.au>

> On 20/06/2012 5:08 PM, James Starlight wrote:
>> Mark,
>> I've made changes in the input mdp file
>> integrator     = md
>> energygrps      = Protein_ADN
>> freezegrps     = Protein_ADN
>> freezedim      = Y Y Y
>> energygrp_table
>> energygrp_excl = Protein_ADN Protein_ADN
>> here Protein_ADN is the protein_ligand defined in the index.mdp
>> than I've processed by grompp without problems
>> but during insertion step by follow command
>> g_membed -f input.tpr -p topol.top -n index.ndx -xyinit 0.1 -xyend 1.0
>> -nxy 1000
>> here I choose Protein_ADN as the group to be inserted and POP as the
>> group wich are membrane. Eventually I've obtained another strange error
>> Moleculetype POP is found both in the group to insert and the rest of the
>> system.
>> Because we need to exclude all interactions between the atoms in the
>> group to
>> insert, the same moleculetype can not be used in both groups. Change the
>> moleculetype of the molecules POP in the inserted group.
>> I've checked my index.ndx and didt not find POP group in my first
>> Protein_ADN group. Why this error should be ?
> Then it seems you're checking things that don't match each other. The
> numbers in the index file must relate to the whole system, defined by the
> [molecules] section. You need to make the index group from a file that
> corresponds to that section, i.e. from the coordinate file you give to
> grompp, which also must match that section. You should note also any
> particular requirements in the g_membed documentation about whether the
> insertion group has to be a single molecule or moleculetype.
> Mark
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