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.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!
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University of Southampton, UK.


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--
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University of Southampton, UK.

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