[gmx-users] g_membed failure
Sophia Kuriakidi
skyriakidi at gmail.com
Wed Sep 21 19:36:45 CEST 2016
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!
>> --
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>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
>
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> Gromacs Users mailing list
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