[gmx-users] g_membed failure
Thomas Piggot
t.piggot at soton.ac.uk
Wed Sep 14 12:56:49 CEST 2016
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.
More information about the gromacs.org_gmx-users
mailing list