[gmx-users] g_membed failure
Tsjerk Wassenaar
tsjerkw at gmail.com
Mon Oct 17 15:26:57 CEST 2016
Hi Sophia,
I can't help out with mdrun -membed, but I did write a tool (insane) to
avoid just the hassle you seem to face. It builds a coarse grained system,
but that can be converted to atomistic. Depending on what exactly you need
to do, it may be trivial or less so. In either case, if you care, you can
contact me offline and we can see whether this could be a useful route for
you.
Best,
Tsjerk
On Mon, Oct 17, 2016 at 1:56 PM, Sophia Kuriakidi <skyriakidi at gmail.com>
wrote:
> Hi again! Anyone with any suggestions? I am totally stuck with this...
>
> 2016-10-03 12:15 GMT+03:00 Sophia Kuriakidi <skyriakidi at gmail.com>:
>
> > Hi Mark,
> >
> > Yes I started with the tutorial you mentioned. From which I understood I
> > need some kind of embed.dat file and that my .mdp file has to have this
> > part:
> > integrator = md
> > energygrps = Protein_Lig (since I have a ligand and I have grouped it
> > with the protein using an index file)
> > freezegrps = Protein_Lig
> > freezedim = Y Y Y
> > energygrp_excl = Protein_Lig Protein_Lig
> >
> > I copied this to the embed file:
> > xyinit (0.5) Resize factor for the protein in the xy dimension before
> > starting embedding.
> > -
> >
> > xyend 1.0
> > zinit 1.0
> > -
> >
> > zend 1.0
> > -
> >
> > nxy 1000
> > -
> >
> > nz 0
> > -
> >
> > rad 0.22
> > -
> >
> > pieces 1
> > -
> >
> > asymmetry no
> > -
> >
> > ndiff 0
> > -
> >
> > maxwarn 0
> > -
> > - Is that correct? And what is the appropriate command in order to
> > actually run the simulation?
> > - I am sorry if I am asking something obvious, I am completely new to
> > gromacs! Thanks!
> >
> > 2016-10-02 19:28 GMT+03:00 Mark Abraham <mark.j.abraham at gmail.com>:
> >
> >> Hi,
> >>
> >> Did you start with
> >> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun
> >> -features.html#running-a-membrane-protein-embedding-simulation?
> >>
> >>
> >> Mark
> >>
> >> On Sun, 2 Oct 2016 17:13 Sophia Kuriakidi <skyriakidi at gmail.com> wrote:
> >>
> >> > Hi again to all of you!
> >> > I am trying to run at last this membrane simulation. I am trying to
> use
> >> the
> >> > -membed option but I can't figure out how to. Can anyone provide me
> >> with an
> >> > example input line? e.g. gmx mdrun -membed -input file -n index.ndx -p
> >> > topol.top -o output file etc ? And also, can anyone provide with an
> >> example
> >> > embed.dat? Thanks a lot in advance!
> >> >
> >> > 2016-09-22 10:38 GMT+03:00 Sophia Kuriakidi <skyriakidi at gmail.com>:
> >> >
> >> > > Thank you so much Tom, I will try that!
> >> > >
> >> > > 2016-09-21 21:11 GMT+03:00 Thomas Piggot <t.piggot at soton.ac.uk>:
> >> > >
> >> > >> g_membed is now part of mdrun, so you would need to use mdrun with
> >> the
> >> > >> -membed option. From mdrun -h:
> >> > >>
> >> > >> /"The option -membed does what used to be g_membed, i.e. embed a
> >> protein
> >> > >> into a//
> >> > >> //membrane. This module requires a number of settings that are
> >> provided
> >> > >> in a//
> >> > >> //data file that is the argument of this option. For more details
> in
> >> > >> membrane//
> >> > >> //embedding, see the documentation in the user guide. The options
> -mn
> >> > and
> >> > >> -mp//
> >> > >> //are used to provide the index and topology files used for the
> >> > >> embedding."/
> >> > >>
> >> > >> Cheers
> >> > >>
> >> > >> Tom
> >> > >>
> >> > >>
> >> > >> On 21/09/16 18:36, Sophia Kuriakidi wrote:
> >> > >>
> >> > >>> Thank you for your responses!
> >> > >>>
> >> > >>> Sotirios:"Also the way this worked for me was to use an index
> file.
> >> I
> >> > >>> made
> >> > >>> an index of the prot + lig + crystallographic waters and I used it
> >> in
> >> > >>> both
> >> > >>> grompp and g_membed. In the latter I just used the group and then
> >> > >>> selected
> >> > >>> the POPC. You must also include the group's name in the mdp in
> order
> >> > for
> >> > >>> it
> >> > >>> to work."
> >> > >>> I also have grouped the ligand with the protein (but not any
> waters)
> >> > and
> >> > >>> I
> >> > >>> included the index in the mdp file.
> >> > >>>
> >> > >>> Thomas:"My guess is that you probably also have an older version
> of
> >> the
> >> > >>> g_membed program installed on your system and as you are trying to
> >> use
> >> > a
> >> > >>> more recent tpr (from version 5.1.2), this might be what is
> causing
> >> the
> >> > >>> segmentation fault. That said, if I try a tpr from GROMACS 5.0.6
> >> with
> >> > >>> g_membed 4.5.7 it does give me a warning about a mismatch of
> >> versions
> >> > so
> >> > >>> I
> >> > >>> could be wrong (but what you say you are doing shouldn't be
> >> possible)."
> >> > >>>
> >> > >>> It seems that this is the case because I am using 5.1.2. How
> could I
> >> > >>> resolve this problem? How coould I use g_membed in 5.1.2? Or how I
> >> > could
> >> > >>> alternatively insert my protein into a membrane bilayer?
> >> > >>>
> >> > >>> Thanks again!
> >> > >>>
> >> > >>>
> >> > >>>
> >> > >>> 2016-09-14 13:47 GMT+03:00 Thomas Piggot <t.piggot at soton.ac.uk>:
> >> > >>>
> >> > >>> Hi,
> >> > >>>>
> >> > >>>> In more recent versions of GROMACS (4.6.x and above IIRC), the
> >> > g_membed
> >> > >>>> feature is only available using mdrun (see mdrun -h) and so the
> >> > g_membed
> >> > >>>> command should either no longer work at all or print you a note
> to
> >> > tell
> >> > >>>> you
> >> > >>>> to use mdrun (depending upon version).
> >> > >>>>
> >> > >>>> My guess is that you probably also have an older version of the
> >> > g_membed
> >> > >>>> program installed on your system and as you are trying to use a
> >> more
> >> > >>>> recent
> >> > >>>> tpr (from version 5.1.2), this might be what is causing the
> >> > segmentation
> >> > >>>> fault. That said, if I try a tpr from GROMACS 5.0.6 with g_membed
> >> > 4.5.7
> >> > >>>> it
> >> > >>>> does give me a warning about a mismatch of versions so I could be
> >> > wrong
> >> > >>>> (but what you say you are doing shouldn't be possible).
> >> > >>>>
> >> > >>>> Cheers
> >> > >>>>
> >> > >>>> Tom
> >> > >>>>
> >> > >>>>
> >> > >>>> On 14/09/16 08:40, Sotirios Dionysios I. Papadatos wrote:
> >> > >>>>
> >> > >>>> Hi, run some diagnostics, don't use the -xyinit etc
> >> > >>>>>
> >> > >>>>> Try the basics gmx g_membed -f -p ... etc
> >> > >>>>>
> >> > >>>>> Also the way this worked for me was to use an index file. I made
> >> an
> >> > >>>>> index
> >> > >>>>> of the prot + lig + crystallographic waters and I used it in
> both
> >> > >>>>> grompp
> >> > >>>>> and g_membed. In the latter I just used the
> >> > >>>>>
> >> > >>>>> group and then selected the POPC. You must also include the
> >> group's
> >> > >>>>> name
> >> > >>>>> in the mdp in order for it to work.
> >> > >>>>>
> >> > >>>>> ________________________________
> >> > >>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> >> > >>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> >> > Sophia
> >> > >>>>> Kuriakidi <skyriakidi at gmail.com>
> >> > >>>>> Sent: Tuesday, September 13, 2016 9:18:12 PM
> >> > >>>>> To: gromacs.org_gmx-users at maillist.sys.kth.se
> >> > >>>>> Subject: [gmx-users] g_membed failure
> >> > >>>>>
> >> > >>>>> Hi all,
> >> > >>>>> I am trying to use g_membed in order to embed my protein in a
> >> lipid
> >> > >>>>> bilayer
> >> > >>>>> (I am using dppc). I am using the tutorial of Appendix A of this
> >> > paper:
> >> > >>>>>
> >> > >>>>> *http://wwwuser.gwdg.de/~ggroenh/submitted/Membed_rev.pdf
> >> > >>>>> <http://wwwuser.gwdg.de/~ggroenh/submitted/Membed_rev.pdf>*
> >> > >>>>>
> >> > >>>>> I am creating an input.tpr using this command:
> >> > >>>>>
> >> > >>>>> grompp -f sample.mdp -c merged.gro -p merged.top -o input.tpr
> >> > >>>>>
> >> > >>>>> and it works fine. Then when I am trying to use g_membed by
> >> typping
> >> > >>>>> this:
> >> > >>>>>
> >> > >>>>> g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy
> >> 1000
> >> > >>>>>
> >> > >>>>> or this
> >> > >>>>>
> >> > >>>>> g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0
> -nxy
> >> > 1000
> >> > >>>>> -zinit 1.1 -zend 1.0 -nz 100
> >> > >>>>>
> >> > >>>>> I just get the g_membed manual printed out...
> >> > >>>>>
> >> > >>>>> $ g_membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0
> -nxy
> >> > 1000
> >> > >>>>> Option Filename Type Description
> >> > >>>>> ------------------------------------------------------------
> >> > >>>>> -f input.tpr Input Run input file: tpr tpb tpa
> >> > >>>>> -n index.ndx Input, Opt. Index file
> >> > >>>>> -p merged.top In/Out, Opt! Topology file
> >> > >>>>> -o traj.trr Output Full precision trajectory:
> trr
> >> > trj
> >> > >>>>> cpt
> >> > >>>>> -x traj.xtc Output, Opt. Compressed trajectory
> >> (portable
> >> > xdr
> >> > >>>>> format)
> >> > >>>>> -cpi state.cpt Input, Opt. Checkpoint file
> >> > >>>>> -cpo state.cpt Output, Opt. Checkpoint file
> >> > >>>>> -c membedded.gro Output Structure file: gro g96 pdb
> >> etc.
> >> > >>>>> -e ener.edr Output Energy file
> >> > >>>>> -g md.log Output Log file
> >> > >>>>> -ei sam.edi Input, Opt. ED sampling input
> >> > >>>>> -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro
> g96
> >> pdb
> >> > >>>>> cpt
> >> > >>>>> -table table.xvg Input, Opt. xvgr/xmgr file
> >> > >>>>> -tablep tablep.xvg Input, Opt. xvgr/xmgr file
> >> > >>>>> -tableb table.xvg Input, Opt. xvgr/xmgr file
> >> > >>>>> -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
> >> > >>>>> -field field.xvg Output, Opt. xvgr/xmgr file
> >> > >>>>> -table table.xvg Input, Opt. xvgr/xmgr file
> >> > >>>>> -tablep tablep.xvg Input, Opt. xvgr/xmgr file
> >> > >>>>> -tableb table.xvg Input, Opt. xvgr/xmgr file
> >> > >>>>> -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro
> g96
> >> pdb
> >> > >>>>> cpt
> >> > >>>>> -tpi tpi.xvg Output, Opt. xvgr/xmgr file
> >> > >>>>> -tpid tpidist.xvg Output, Opt. xvgr/xmgr file
> >> > >>>>> -ei sam.edi Input, Opt. ED sampling input
> >> > >>>>> -eo sam.edo Output, Opt. ED sampling output
> >> > >>>>> -j wham.gct Input, Opt. General coupling stuff
> >> > >>>>> -jo bam.gct Output, Opt. General coupling stuff
> >> > >>>>> -ffout gct.xvg Output, Opt. xvgr/xmgr file
> >> > >>>>> -devout deviatie.xvg Output, Opt. xvgr/xmgr file
> >> > >>>>> -runav runaver.xvg Output, Opt. xvgr/xmgr file
> >> > >>>>> -px pullx.xvg Output, Opt. xvgr/xmgr file
> >> > >>>>> -pf pullf.xvg Output, Opt. xvgr/xmgr file
> >> > >>>>> -mtx nm.mtx Output, Opt. Hessian matrix
> >> > >>>>> -dn dipole.ndx Output, Opt. Index file
> >> > >>>>>
> >> > >>>>> Option Type Value Description
> >> > >>>>> ------------------------------------------------------
> >> > >>>>> -[no]h bool no Print help info and quit
> >> > >>>>> -[no]version bool no Print version info and quit
> >> > >>>>> -nice int 0 Set the nicelevel
> >> > >>>>> -deffnm string Set the default filename for all
> file
> >> > >>>>> options
> >> > >>>>> -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr
> or
> >> > none
> >> > >>>>> -xyinit real 0.1 Resize factor for the protein in the
> >> xy
> >> > >>>>> dimension
> >> > >>>>> before starting embedding
> >> > >>>>> -xyend real 1 Final resize factor in the xy
> >> dimension
> >> > >>>>> -zinit real 1 Resize factor for the protein in
> the z
> >> > >>>>> dimension
> >> > >>>>> before starting embedding
> >> > >>>>> -zend real 1 Final resize faction in the z
> >> dimension
> >> > >>>>> -nxy int 1000 Number of iteration for the xy
> >> dimension
> >> > >>>>> -nz int 0 Number of iterations for the z
> >> dimension
> >> > >>>>> -rad real 0.22 Probe radius to check for overlap
> >> between
> >> > >>>>> the
> >> > >>>>> group to embed and the membrane
> >> > >>>>> -pieces int 1 Perform piecewise resize. Select
> >> parts of
> >> > >>>>> the
> >> > >>>>> group to insert and resize these
> >> with
> >> > >>>>> respect to
> >> > >>>>> their own geometrical center.
> >> > >>>>> -[no]asymmetry bool no Allow asymmetric insertion, i.e. the
> >> > >>>>> number of
> >> > >>>>> lipids removed from the upper and
> >> lower
> >> > >>>>> leaflet
> >> > >>>>> will not be checked.
> >> > >>>>> -ndiff int 0 Number of lipids that will
> >> additionally
> >> > be
> >> > >>>>> removed from the lower (negative
> >> > number)
> >> > >>>>> or
> >> > >>>>> upper
> >> > >>>>> (positive number) membrane
> leaflet.
> >> > >>>>> -maxwarn int 0 Maximum number of warning allowed
> >> > >>>>> -[no]compact bool yes Write a compact log file
> >> > >>>>> -[no]v bool no Be loud and noisy
> >> > >>>>>
> >> > >>>>>
> >> > >>>>> Back Off! I just backed up md.log to ./#md.log.2#
> >> > >>>>> Reading file input.tpr, VERSION 5.1.2 (single precision*)*
> >> > >>>>> *Segmentation fault (core dumped)*
> >> > >>>>>
> >> > >>>>> Along with this highlighted message...
> >> > >>>>>
> >> > >>>>> I can't figure out what's wrong, please I could use some help!
> >> > >>>>> --
> >> > >>>>> Gromacs Users mailing list
> >> > >>>>>
> >> > >>>>> * Please search the archive at http://www.gromacs.org/Support
> >> > >>>>> /Mailing_Lists/GMX-Users_List before posting!
> >> > >>>>>
> >> > >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> > >>>>>
> >> > >>>>> * For (un)subscribe requests visit
> >> > >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
> >> -users
> >> > or
> >> > >>>>> send a mail to gmx-users-request at gromacs.org.
> >> > >>>>>
> >> > >>>>> --
> >> > >>>> Dr Thomas Piggot
> >> > >>>> Visiting Fellow
> >> > >>>> University of Southampton, UK.
> >> > >>>>
> >> > >>>>
> >> > >>>> --
> >> > >>>> Gromacs Users mailing list
> >> > >>>>
> >> > >>>> * Please search the archive at http://www.gromacs.org/Support
> >> > >>>> /Mailing_Lists/GMX-Users_List before posting!
> >> > >>>>
> >> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> > >>>>
> >> > >>>> * For (un)subscribe requests visit
> >> > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> >> or
> >> > >>>> send a mail to gmx-users-request at gromacs.org.
> >> > >>>>
> >> > >>>>
> >> > >> --
> >> > >> Dr Thomas Piggot
> >> > >> Visiting Fellow
> >> > >> University of Southampton, UK.
> >> > >>
> >> > >> --
> >> > >> Gromacs Users mailing list
> >> > >>
> >> > >> * Please search the archive at http://www.gromacs.org/Support
> >> > >> /Mailing_Lists/GMX-Users_List before posting!
> >> > >>
> >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> > >>
> >> > >> * For (un)subscribe requests visit
> >> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >> or
> >> > >> send a mail to gmx-users-request at gromacs.org.
> >> > >>
> >> > >
> >> > >
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-request at gromacs.org.
> >> >
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
Tsjerk A. Wassenaar, Ph.D.
More information about the gromacs.org_gmx-users
mailing list