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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