[gmx-users] Insertion protein in the membrane via G_membed
Peter C. Lai
pcl at uab.edu
Wed Jun 20 23:58:26 CEST 2012
My suggestion is to either add the ligand back in after g_membed removes it
or to not g_membed the system with the ligand, if it is acceptable. (Is your
ligand supposed to interact with the bilayer in any meaningful way?)
Or don't use g_membed and fall back to inflatgro for insertion.
On 2012-06-20 12:40:30PM +0400, James Starlight wrote:
> 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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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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