Thank you so much Tom, I will try that!

2016-09-21 21:11 GMT+03:00 Thomas Piggot <t.pig...@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.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!
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>
>>>> --
>>> Dr Thomas Piggot
>>> Visiting Fellow
>>> University of Southampton, UK.
>>>
>>>
>>> --
>>> Gromacs Users mailing list
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>>> * Please search the archive at http://www.gromacs.org/Support
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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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