[gmx-users] g_membed failure
Sophia Kuriakidi
skyriakidi at gmail.com
Mon Oct 17 13:56:47 CEST 2016
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!
>> > >>>>
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>> 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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>> or
>> > >> send a mail to gmx-users-request at gromacs.org.
>> > >>
>> > >
>> > >
>> > --
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>> >
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>> > posting!
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