[gmx-users] Insertion protein in the membrane via G_membed
Mark.Abraham at anu.edu.au
Wed Jun 20 10:01:17 CEST 2012
On 20/06/2012 5:08 PM, James Starlight wrote:
> I've made changes in the input mdp file
> integrator = md
> energygrps = Protein_ADN
> freezegrps = Protein_ADN
> freezedim = Y Y Y
> 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.
More information about the gromacs.org_gmx-users