[gmx-users] g_membed failure
Sophia Kuriakidi
skyriakidi at gmail.com
Mon Oct 3 11:15:42 CEST 2016
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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> > >>>>
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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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> > >> send a mail to gmx-users-request at gromacs.org.
> > >>
> > >
> > >
> > --
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> >
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> > posting!
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