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> >
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