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 > ligands > > 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 > embed. > > 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_table > energygrp_excl = Protein Protein > > In that case I have no such problem but during insertion G_membed has > deleted ADN. > > James > > > > 2012/6/20 Mark Abraham <mark.abra...@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 > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > > Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > > posting! > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read > > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
