[gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 62
Bhupendra Dandekar
bhupendra.dandekar001 at gmail.com
Sun Oct 28 12:50:07 CET 2018
Hi Farial,
Do not run acpype like this using python "python acpype.py -i XXX.pdb -b
XXX -o gmx".
Just type only *acpype -h* in the terminal and check whether it is
installed or not?.
If it is working,
Then write the command like this:
*acpype -i FFF.pdb -b FFF -o gmx*
*No python command before the acpype.*
Please, Let me know again if you need any help.
Thanks
On Sun, Oct 28, 2018 at 3:26 PM Farial Tavakoli <faryal.tavakoli at gmail.com>
wrote:
> 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
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > 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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> > > > > >> > >
> > > > > >> > --
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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
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> > before
> > > > > >> posting!
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> > > or
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> > > > > >
> > > > > >
> > > > > --
> > > > > Gromacs Users mailing list
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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
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> > > > posting!
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> > > --
> > > Gromacs Users mailing list
> > >
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> > > 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
> >
> >
> > ------------------------------
> >
> > 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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> > End of gromacs.org_gmx-users Digest, Vol 174, Issue 62
> > ******************************************************
> >
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