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 freezegrps = Protein ADN freezedim = Y Y Y energygrp_table energygrp_excl = Protein Protein here ADN is the ligand than I've tried to generate input file for g_membed where I've selected my protein_ligand group to be inserted into membrane but I've obtained this eror althought protein_ligand group were presented in the list of aviable groups for insertion Fatal error: Group Protein_ADN not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Finally If I've tried to insert kust protein intoi membrane than G_membed delete my ligand during insertion Will remove 0 Protein molecules Will remove 1 ADN molecules Will remove 10 POP molecules Will remove 41 SOL molecules How I could fix this problem and obtain whole protein_ligand system inserted in the membrane ? James 2012/6/15 James Starlight <jmsstarli...@gmail.com> > 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 > inclussion of the same X-ray waters but in different system with > membrane-mimicking env. consisted of Ccl4 in water. As the result there > have not been any problems with that system. > > Finally I have some question about G_membed acceleration. I've noticed > that the process of insertion of the protein in the membrane is very long > (actually it's only 50ps simulation). > > During procesing of my system I've obtained notes like > > NOTE 4 [file topol.top, line 19511]: > For energy conservation with LINCS, lincs_iter should be 2 or larger. > > NOTE 1 [file gmembed.mdp]: > You are using a cut-off for VdW interactions with NVE, for good energy > conservation use vdwtype = Shift (possibly with DispCorr) > > NOTE 2 [file gmembed.mdp]: > You are using a cut-off for electrostatics with NVE, for good energy > conservation use coulombtype = PME-Switch or Reaction-Field-zero > > The parameters for long-range and short-range interactions I've used from > my typical simulation on the lipid Gromos56-ff ( presented in the Justin's > tutorial). > > Is there any other parameters for that object wich are most suitable for > G_membed ? > > James > > > > 2012/6/14 James Starlight <jmsstarli...@gmail.com> > >> 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 lipids in the membrane part that overlaps the protein. >> The area per lipid is 0.5002 nm^2. >> Maximum number of lipids that will be removed is 45. >> >> and eventually only 10 lipids were removed. Also I've tried to do this on >> another pope bilayer (consisted of bigger lipids with properly equilirated >> ) but I've obtained exactly the same results. >> >> >> James >> >> 2012/6/14 Mark Abraham <mark.abra...@anu.edu.au> >> >>> 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 dimensions merged both >>> topologies and gro files in the merged.gro file ) but after processed via >>> grompp I've recieved warning >>> >>> WARNING 1 [file gmembed.mdp]: >>> Can not exclude the lattice Coulomb energy between energy groups >>> >>> >>> You've asked about this before... >>> http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html >>> >>> >>> if I scip this message by maxwarn oprtins, g_membed remove only 10 >>> lipids ( while > 40 are overlapped with the protein ) and during further >>> g_membed's md_run I've obtained lincs warning and my system is crushed . >>> >>> >>> Have you followed g_membed -h and their published method? You've not >>> shown your command lines, so it's impossible for anyone to know what you're >>> doing. >>> >>> Mark >>> >>> >>> >>> >>> I'm using berger lipids and that mdp file for the G_membed >>> >>> integrator = md >>> energygrps = Protein >>> freezegrps = Protein >>> freezedim = Y Y Y >>> energygrp_table >>> energygrp_excl = Protein Protein >>> >>> >>> >>> emtol = 1000.0 ; Stop minimization when the maximum force < >>> 1000.0 kJ/mol/nm >>> emstep = 0.01 ; Energy step size >>> nsteps = 50000 ; Maximum number of (minimization) steps >>> to perform >>> >>> ; Bond parameters >>> constraint_algorithm = lincs ; holonomic constraints >>> constraints = all-bonds ; all bonds (even heavy atom-H >>> bonds) constrained >>> lincs_iter = 1 ; accuracy of LINCS >>> lincs_order = 4 ; also related to accuracy >>> ; Neighborsearching >>> ns_type = grid ; search neighboring grid cels >>> nstlist = 5 ; 10 fs >>> rlist = 1.2 ; short-range neighborlist cutoff (in nm) >>> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) >>> rvdw = 1.2 ; short-range van der Waals cutoff (in nm) >>> ; Electrostatics >>> coulombtype = PME ; Particle Mesh Ewald for long-range >>> electrostatics >>> pme_order = 4 ; cubic interpolation >>> fourierspacing = 0.16 ; grid spacing for FFT >>> pbc = xyz ; 3-D PBC >>> >>> >>> Could you tell me where is the problem in my case might be? >>> >>> >>> James >>> >>> >>> >>> >>> -- >>> 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 >>> >> >> >
-- 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