[gmx-users] g_membed failure

[Sotirios Dionysios I. Papadatos]

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!
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