Re: [gmx-users] Insertion protein in the membrane via G_membed

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

Re: [gmx-users] Insertion protein in the membrane via G_membed

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 t

Re: [gmx-users] Insertion protein in the membrane via G_membed

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 defi

Re: [gmx-users] Insertion protein in the membrane via G_membed

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 gro

Re: [gmx-users] Insertion protein in the membrane via G_membed

On 20/06/2012 4:39 PM, James Starlight wrote: by the way I've forced with problems during insertion of the complex protein_ligand into membrane by means of g_membed firstly I've created index.ndx file with the merged protein_ligand group. Than I've used next mdp for my g_membed input integra

Re: [gmx-users] Insertion protein in the membrane via G_membed

by the way I've forced with problems during insertion of the complex protein_ligand into membrane by means of g_membed firstly I've created index.ndx file with the merged protein_ligand group. Than I've used next mdp for my g_membed input integrator = md energygrps = Protein ADN freezegr

Re: [gmx-users] Insertion protein in the membrane via G_membed

I've found main reason of such crushes. It was due to the individual internal waters wich I've included to my model as the buried to the protein interiour ( the coordinates were copppied form X-ray structure of the same protein). By the way I have already performed the same simulation with the in

Re: [gmx-users] Insertion protein in the membrane via G_membed

Mark, I've used commands provided in the G_membed manual g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000 or g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100 In both cases I've obtained the same message There are 122

Re: [gmx-users] Insertion protein in the membrane via G_membed

On 14/06/2012 4:39 PM, James Starlight wrote: Dear Gromacs Users! I've forced with the problem durin insertion of my protein into pre-equilibrated bilayer via G_Membed. I've done all steps in accordance to the KALP tutorial ( I've oriented both membrane as well as the protein in the same dim

[gmx-users] Insertion protein in the membrane via G_membed

Dear Gromacs Users! I've forced with the problem durin insertion of my protein into pre-equilibrated bilayer via G_Membed. I've done all steps in accordance to the KALP tutorial ( I've oriented both membrane as well as the protein in the same dimensions merged both topologies and gro files in the