[gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 71
Bhupendra Dandekar
bhupendra.dandekar001 at gmail.com
Mon Oct 29 11:59:04 CET 2018
Please install anaconda3 first.
Delete your previous anconda2 from your home.
Simply download install script from anaconda website.
and the run it using bash Anaconda---
Then let me know
Thanks
Bhupendra
On Mon, Oct 29, 2018 at 4:22 PM Farial Tavakoli <faryal.tavakoli at gmail.com>
wrote:
> Hi Bhupendra
>
> yes i am on lone now.
>
> Farial
>
> On Mon, Oct 29, 2018 at 2:11 PM <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
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> > Today's Topics:
> >
> > 1. Error of CgenFF convert to itp (Mijiddorj B)
> > 2. acpype and conda (Farial Tavakoli)
> > 3. Re: acpype and conda (Bhupendra Dandekar)
> > 4. Place a gap in y-axis (Raag Saluja)
> > 5. Selection of residues in one of the chains of heterodimer
> > (Raag Saluja)
> > 6. Temperature in CG production runs (Yasser Almeida Hern?ndez)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 29 Oct 2018 12:04:48 +0900
> > From: Mijiddorj B <b.mijiddorj at gmail.com>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] Error of CgenFF convert to itp
> > Message-ID:
> > <
> > CABgRApuGYqmdqtsAXd-xOmWrVFhAZQuWGkLtxpejCx3FOmg68w at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > I would like to generate parameters for small molecule using CGenFF. I
> > generated str file using cgenFF. However, I could not convert to itp file
> > using cgenff_charmm2gmx.py because of following error:
> > Please advice me.
> >
> > NOTE2: Please be sure to use the same version of CGenFF in your
> simulations
> > that was used during parameter generation:
> > --Version of CGenFF detected in mol.str : 4.0
> > --Version of CGenFF detected in charmm36.ff/forcefield.doc : 4.0
> >
> > NOTE3: In order to avoid duplicated parameters, do NOT select the
> 'Include
> > parameters that are already in CGenFF' option when uploading a molecule
> > into CGenFF.
> > Traceback (most recent call last):
> > File "./cgenff_charmm2gmx.py", line 799, in <module>
> > m.read_charmm_rtp(rtplines,atomtypes)
> > File "./cgenff_charmm2gmx.py", line 540, in read_charmm_rtp
> > self.G.add_node(self.natoms, atm[self.natoms])
> > TypeError: add_node() takes exactly 2 arguments (3 given)
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 29 Oct 2018 10:09:41 +0330
> > From: Farial Tavakoli <faryal.tavakoli at gmail.com>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] acpype and conda
> > Message-ID:
> > <
> > CADMAFqEU45d30NK734Ffij4NEXNyfr5D8NgJRMRFsigovsMzHA at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Dear Bhupendra
> >
> > Thanks for your reply
> >
> > I am in /Downloads/acpype-master/acpype/scripts path and type only acpype
> > -h or acpype.py -h , but face with this error:
> > acpype: command not found
> > I can run acpype only when type python command before it.
> > In addition, I installed Anaconda2-5.3.0-Linux-x86_64.sh on "/home/vaio"
> > yesterday and issued the "conda install -c acpype -c openbabel -c
> ambermd"
> > command
> > but faced with this error:
> > CondaValueError: too few arguments, must supply command line package
> specs
> > or --file
> > python version = python 2.7.15
> > Would you please help me ? I dont know how I should deal with these
> > problems.
> >
> > Thanks in advance
> > Farial
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 29 Oct 2018 12:26:26 +0530
> > From: Bhupendra Dandekar <bhupendra.dandekar001 at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] acpype and conda
> > Message-ID:
> > <CA+jgKGWasQv2b9ckMLE5Ui4CbOcTmwrmxg1Eoe0=
> > mK1Mb-DKRw at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi Farial,
> > Are you online now?
> >
> > Bhupendra
> >
> > On Mon, Oct 29, 2018 at 12:10 PM Farial Tavakoli <
> > faryal.tavakoli at gmail.com>
> > wrote:
> >
> > > Dear Bhupendra
> > >
> > > Thanks for your reply
> > >
> > > I am in /Downloads/acpype-master/acpype/scripts path and type only
> acpype
> > > -h or acpype.py -h , but face with this error:
> > > acpype: command not found
> > > I can run acpype only when type python command before it.
> > > In addition, I installed Anaconda2-5.3.0-Linux-x86_64.sh on
> "/home/vaio"
> > > yesterday and issued the "conda install -c acpype -c openbabel -c
> > ambermd"
> > > command
> > > but faced with this error:
> > > CondaValueError: too few arguments, must supply command line package
> > specs
> > > or --file
> > > python version = python 2.7.15
> > > Would you please help me ? I dont know how I should deal with these
> > > problems.
> > >
> > > Thanks in advance
> > > Farial
> > > --
> > > 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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> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Mon, 29 Oct 2018 13:25:35 +0530
> > From: Raag Saluja <saluja.raag at gmail.com>
> > To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> > <gromacs.org_gmx-users at maillist.sys.kth.se>
> > Subject: [gmx-users] Place a gap in y-axis
> > Message-ID:
> > <CALwqOC7J99UZmENfwFMoiVQPRJ=G0wYOMxpprFdO-=
> > 70OKzhSw at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi! This is not really a gromacs question, but I was wondering if you
> could
> > help, please!
> >
> > I have a multiple line plot with a major difference between one of the
> > plots and the rest. Hence, I need to insert a gap in the y axis. I
> usually
> > use grace to plot the graphs generated by gromacs, but I?m unable to
> place
> > the gap in the y axis in grace. Could you please help?
> >
> > Thank you in advance!
> > Regards,
> > Raag
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Mon, 29 Oct 2018 14:15:54 +0530
> > From: Raag Saluja <saluja.raag at gmail.com>
> > To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> > <gromacs.org_gmx-users at maillist.sys.kth.se>
> > Subject: [gmx-users] Selection of residues in one of the chains of
> > heterodimer
> > Message-ID:
> > <
> > CALwqOC46omibrPzrjJ0b1okkcG5XmmmJOC9nrknzp7BM384xxg at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi!
> >
> > I simulated a heterodimer and converted the md.gro file into a pdb file.
> > This pdb file I visualised in vmd. I wish to select residues (first 50,
> > then next 50 and so on), so that I can correlate the structure with the
> > graphs obtained by structure analysis.
> > If I give the command resid 1 to 50 and protein, the first 50 residues of
> > both chains are selected.
> > If I give the command resid 1 to 50 and protein and chain A, it works
> with
> > the original file obtained from protein data bank. However, with the
> > simulated protein?s pdb file, the area just gets deselected.
> > Can you please help?
> > Thank you in advance!
> > Regards,
> > Raag
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Mon, 29 Oct 2018 11:34:47 +0100
> > From: Yasser Almeida Hern?ndez
> > <yasser.almeida.hernandez at chemie.uni-hamburg.de>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] Temperature in CG production runs
> > Message-ID:
> > <0234af1e-6430-3a9f-683f-5cd5b69d0d3b at chemie.uni-hamburg.de>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> > Dear all,
> >
> > I am performing CG simulations (Martini) of a membrane protein in an
> > heterogeneous model bilayer with several lipids, resembling the inner
> > membrane from E. coli.
> >
> > Looking in the literature, I have seen that the temperature for
> > production runs range from 300-330K, which are a big difference in
> > physiological terms. What temperature would you recommend in my case?
> >
> > Thanks in advance and best regards
> >
> > Yasser
> >
> > --
> > Yasser Almeida Hern?ndez
> > PhD student
> > Institute of Biochemistry and Molecular Biology
> > Department of Chemistry
> > University of Hamburg
> > Martin-Luther-King-Platz 6
> > 20146 Hamburg
> > Germany
> > +49 40 42838 2845
> > yasser.almeida.hernandez at chemie.uni-hamburg.de
> > office: Grindelallee 117, room 250c
> >
> >
> >
> > ------------------------------
> >
> > --
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> > End of gromacs.org_gmx-users Digest, Vol 174, Issue 71
> > ******************************************************
> >
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