[gmx-users] g_membed failure
Sophia Kuriakidi
skyriakidi at gmail.com
Thu Sep 22 09:38:48 CEST 2016
Thank you so much Tom, I will try that!
2016-09-21 21:11 GMT+03:00 Thomas Piggot <t.piggot at soton.ac.uk>:
> 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.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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>>>>
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>>>> --
>>> Dr Thomas Piggot
>>> Visiting Fellow
>>> University of Southampton, UK.
>>>
>>>
>>> --
>>> Gromacs Users mailing list
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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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