[gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 71
Farial Tavakoli
faryal.tavakoli at gmail.com
Mon Oct 29 11:51:47 CET 2018
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:
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> 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!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > 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
>
>
>
> ------------------------------
>
> --
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 174, Issue 71
> ******************************************************
>
More information about the gromacs.org_gmx-users
mailing list