[gmx-users] g_membed failure
Mark Abraham
mark.j.abraham at gmail.com
Sun Oct 2 18:29:05 CEST 2016
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!
> >>>>
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> >>>> 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!
> >>
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> >>
> >
> >
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