[gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 62
Farial Tavakoli
faryal.tavakoli at gmail.com
Sun Oct 28 10:55:28 CET 2018
Dear Bhupendra
I installed anaconda on /home/vaio/ and then issued the same command that
you wrote
conda install -c acpype -c openbabel -c ambermd
but faced with this error:
CondaValueError: too few arguments, must supply command line package specs
or --file
the python version that I have, is python 2.7.15
Would you please help me ? I dont understand what the problem is?
Thanks in advance
Farial
On Thu, Oct 25, 2018 at 1:31 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: How to generate a new xtc file with a membrane protein
> complex properly oriented along a given axis? (Dallas Warren)
> 2. Re: acpype (Alan)
> 3. Re: gmx kill computer? (Harry Mark Greenblatt)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 25 Oct 2018 07:43:25 +1100
> From: Dallas Warren <dallas.warren at monash.edu>
> To: GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] How to generate a new xtc file with a
> membrane protein complex properly oriented along a given axis?
> Message-ID:
> <
> CAOv1qzZfqB2pMNCXOkF2KqrNrOGHG4-PdE7pXps96VqzUMZhuQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Haven't tried it, but seems to me you generate a .tpr file with the
> protein orientated correctly within the box, then use trjconv -fit
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
> On Wed, 24 Oct 2018 at 20:38, ABEL Stephane <Stephane.ABEL at cea.fr> wrote:
> >
> > Hello All,
> >
> > I have basic questions regarding the procedure to generate an new xtc
> where a membrane protein inserted a detergent micelle is properly oriented
> for the computation of 2D density Map. Indeed for this calculation I need
> to have the protein-surfactant complex properly oriented along a given axis
> (say Z). For this I chose two atoms and define a vector in my protein and I
> would like that this vector // to z axis. How to this in GROMACS? I think
> that editconf can do the trick, however I notice that this tool cannot use
> and output an xtc file. So is there an alternative approach ? If yes how
> (an example of command line will be very useful)
> >
> > Thanks in advance
> >
> > Stephane
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> posting!
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>
> ------------------------------
>
> Message: 2
> Date: Wed, 24 Oct 2018 22:28:33 +0100
> From: Alan <alanwilter at gmail.com>
> To: Gromacs <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] acpype
> Message-ID:
> <
> CAEznbznwV_9AUinPskanDWtTVsH0-XM-yOfXsoD-YnJYJoVivA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> We are working on it now. I can't tell you exactly because we need several
> tests. It's a complete new version re-written from scratch.
>
> I'm really sorry for the inconvenience but we hope to bring it back in a
> month or two.
>
> Alan
>
> On Wed, 24 Oct 2018 at 16:58, neelam wafa <neelam.wafa at gmail.com> wrote:
>
> > Hi alan
> >
> > Can you please tell how long will it take for the online acpype server to
> > be available?
> >
> > Regards
> > Neelam wafa
> >
> > On Wed, 24 Oct 2018, 6:23 pm Alan, <alanwilter at gmail.com> wrote:
> >
> > > Indeed, it's mostly Luciano spearheading these new things. Hopefully,
> we
> > > will have more things to show eventually.
> > >
> > > Alan
> > >
> > > On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar <
> > > bhupendra.dandekar001 at gmail.com> wrote:
> > >
> > > > I actually got lot of help from Luciano Kagami about installation and
> > > usage
> > > > of acpype and ligro.
> > > > Thanks to both of you.
> > > >
> > > > Bhupendra
> > > >
> > > > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
> > > > bhupendra.dandekar001 at gmail.com> wrote:
> > > >
> > > > > Thanks to you also sir.
> > > > > Your work is really appreciated and is really helpful.
> > > > >
> > > > >
> > > > > Bhupendra
> > > > >
> > > > > On Wed, Oct 24, 2018 at 3:59 PM Alan <alanwilter at gmail.com> wrote:
> > > > >
> > > > >> Thanks Bhupendra, indeed we have this option, which is
> experimental,
> > > but
> > > > >> I'm glad to see some are already using it and it seems to be
> > working.
> > > > >>
> > > > >> Alan
> > > > >>
> > > > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> > > > >> bhupendra.dandekar001 at gmail.com> wrote:
> > > > >>
> > > > >> > Dear Farial,
> > > > >> >
> > > > >> > Use this command to install acpype and antechamber using conda:
> > > > >> >
> > > > >> > conda install -c acpype -c openbabel -c ambermd
> > > > >> >
> > > > >> > and then you can check and call acpype, antechamber like this
> from
> > > > your
> > > > >> > terminal:
> > > > >> >
> > > > >> > acpype -h
> > > > >> > antechamber -h
> > > > >> >
> > > > >> > then you can generate ligand topology using this command:
> > > > >> >
> > > > >> > acpype -i FFF.pdb -b FFF -o gmx
> > > > >> >
> > > > >> > Hope this helps. Let me know if you have any questions.
> > > > >> >
> > > > >> > Thanks
> > > > >> > Bhupendra
> > > > >> >
> > > > >> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <
> > > > >> faryal.tavakoli at gmail.com
> > > > >> > >
> > > > >> > wrote:
> > > > >> >
> > > > >> > > Dear GMX useres
> > > > >> > >
> > > > >> > > I am trying to convert .OFF and .FRCMOD files obtained from
> > AMBER
> > > > >> > parameter
> > > > >> > > database (Bryce Group: Computational Biophysics and Drug
> Design
> > -
> > > > >> > > University of Manchester)
> > > > >> > > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the
> > > format
> > > > >> that
> > > > >> > > GROMACS is compatible with in .rtp files*. so referred to
> > GROMACS
> > > > >> > tutorial
> > > > >> > > protein-ligand complex and downloaded acpype. installed it
> using
> > > its
> > > > >> > > readme.txt file but whenever i typed ../acpype.py -i
> FFF.pdb
> > > At
> > > > >> > folder
> > > > >> > > *acpype/test* (/Downloads/acpype-master/acpype) or
> > > > >> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> > > > >> > >
> > > > >> > >
> > > > >> > > *bash: ../acpype.py: No such file or directory*
> > > > >> > >
> > > > >> > > *while when I typed whereis acpype in terminal , the operating
> > > > system
> > > > >> > says
> > > > >> > > :*
> > > > >> > >
> > > > >> > >
> > > > >> > > *acpype: /usr/local/bin/acpype*
> > > > >> > > * it means there is the executable file of acpype . so how
> come
> > I
> > > > type
> > > > >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO
> > such
> > > > >> file or
> > > > >> > > directory?*
> > > > >> > > *Is there anyone who ca help me?*
> > > > >> > > *I really would be appreciated it if one help me to solve this
> > and
> > > > can
> > > > >> > > convert the AMBER format files to GRMACS format files.*
> > > > >> > >
> > > > >> > > *best regards*
> > > > >> > > *Farial*
> > > > >> > > --
> > > > >> > > Gromacs Users mailing list
> > > > >> > >
> > > > >> > > * Please search the archive at
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> > > before
> > > > >> > > posting!
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> > > > or
> > > > >> > > send a mail to gmx-users-request at gromacs.org.
> > > > >> > >
> > > > >> > --
> > > > >> > Gromacs Users mailing list
> > > > >> >
> > > > >> > * Please search the archive at
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> > before
> > > > >> > posting!
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> > > > >> >
> > > > >>
> > > > >>
> > > > >> --
> > > > >> *I**? have just cycled* from Land's End to John O'Groats??? (the
> > > > >> whole Britain!)
> > > > >> for a charity, would you consider? ?supporting my? cause?
> > > > >> http://uk.virginmoneygiving.com/AlanSilva
> > > > >> --
> > > > >> Alan Wilter SOUSA da SILVA, DSc
> > > > >> Senior Bioinformatician, UniProt
> > > > >> European Bioinformatics Institute (EMBL-EBI)
> > > > >> European Molecular Biology Laboratory
> > > > >> Wellcome Trust Genome Campus
> > > > >> Hinxton
> > > > >> Cambridge CB10 1SD
> > > > >> United Kingdom
> > > > >> Tel: +44 (0)1223 494588
> > > > >> --
> > > > >> 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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> > > > >>
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> > > > >>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > >> send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
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> > >
> > >
> > >
> > > --
> > > *I**? have just cycled* from Land's End to John O'Groats??? (the
> > > whole Britain!)
> > > for a charity, would you consider? ?supporting my? cause?
> > > http://uk.virginmoneygiving.com/AlanSilva
> > > --
> > > Alan Wilter SOUSA da SILVA, DSc
> > > Senior Bioinformatician, UniProt
> > > European Bioinformatics Institute (EMBL-EBI)
> > > European Molecular Biology Laboratory
> > > Wellcome Trust Genome Campus
> > > Hinxton
> > > Cambridge CB10 1SD
> > > United Kingdom
> > > Tel: +44 (0)1223 494588
> > > --
> > > 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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> > >
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> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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>
>
>
> --
> *I**? have just cycled* from Land's End to John O'Groats??? (the
> whole Britain!)
> for a charity, would you consider? ?supporting my? cause?
> http://uk.virginmoneygiving.com/AlanSilva
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 25 Oct 2018 06:55:22 +0000
> From: Harry Mark Greenblatt <harry.greenblatt at weizmann.ac.il>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] gmx kill computer?
> Message-ID: <A6EEFCFF-B952-4F03-A335-D31135951070 at weizmann.ac.il>
> Content-Type: text/plain; charset="utf-8"
>
> BS?D
>
> Dear Michael,
>
> ThermalTake PSU?s are better than many out there, but they aren?t the
> best. Here is a link discussing how the theoretical wattage rating of a
> PSU may not actually translate into enough watts in reality, especially
> under sustained load.
>
> http://www.tomshardware.com/forum/285455-28-problem-thermaltake-750w
>
>
> Nevertheless, I am a bit surprised that your PSU?s can?t handle a GTX 1060.
>
> Since both machines are doing the same thing, and have very different
> hardware, except for the graphics cards and the PSU, it does seem to point
> a finger at the PSU. Since both are failing, that further suggests that the
> model of PSU is problematic, as opposed to them being truly faulty.
>
> Again, try and swap one with a different manufacturer, if possible.
>
> Good luck,
>
> Harry
>
>
>
> On 24 Oct 2018, at 12:06 PM, Michael Brunsteiner <mbx0009 at yahoo.com
> <mailto:mbx0009 at yahoo.com>> wrote:
>
> Hi,
>
> Thanks for you replies, Harry and Mirco!I've got 700W Thermaltake PSUs
> here ... according to several web-sites thatcalculate the expected power
> consumption for a given set of components, and alsoin our experience this
> should be more than enough ...Can it be that, as Mirco suggested, the 1060
> in combination with gmx can give particularlylarge spikes or changes in
> energy consumption so that even a 700W PSU cannot cope?
> cheers,michael
>
>
>
> --------------------------------------------------------------------
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology harry.greenblatt at weizmann.ac.il
> <mailto:harry.greenblatt at weizmann.ac.il>
> Weizmann Institute of Science Phone: 972-8-934-6340
> 234 Herzl St. Facsimile: 972-8-934-3361
> Rehovot, 7610001
> Israel
>
>
> ------------------------------
>
> --
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