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.pig...@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-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sophia
>> Kuriakidi <skyriak...@gmail.com>
>> Sent: Tuesday, September 13, 2016 9:18:12 PM
>> To: gromacs.org_gmx-users@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
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>>
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>>
>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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