[gmx-users] g_membed failure

Thomas Piggot t.piggot at soton.ac.uk
Wed Sep 21 20:19:33 CEST 2016


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
>>>
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>>>
>> --
>> 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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>>

-- 
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.



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