[gmx-users] g_membed failure
Sophia Kuriakidi
skyriakidi at gmail.com
Sun Oct 2 17:13:00 CEST 2016
Hi again to all of you!
I am trying to run at last this membrane simulation. I am trying to use the
-membed option but I can't figure out how to. Can anyone provide me with an
example input line? e.g. gmx mdrun -membed -input file -n index.ndx -p
topol.top -o output file etc ? And also, can anyone provide with an example
embed.dat? Thanks a lot in advance!
2016-09-22 10:38 GMT+03:00 Sophia Kuriakidi <skyriakidi at gmail.com>:
> 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!
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>> --
>>>> Dr Thomas Piggot
>>>> Visiting Fellow
>>>> University of Southampton, UK.
>>>>
>>>>
>>>> --
>>>> 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
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>>>>
>>>>
>> --
>> Dr Thomas Piggot
>> Visiting Fellow
>> University of Southampton, UK.
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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