Hi Bhupendra yes i am on lone now.
Farial On Mon, Oct 29, 2018 at 2:11 PM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@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-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@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.mijidd...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Error of CgenFF convert to itp > Message-ID: > < > cabgrapugyqmdqtsaxd-xomwrvfhazquwgkltxpejcx3fomg...@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.tavak...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] acpype and conda > Message-ID: > < > cadmafqeu45d30nk734ffij4nexnyfr5d8ngjrmrfsigovsm...@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.dandekar...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] acpype and conda > Message-ID: > <CA+jgKGWasQv2b9ckMLE5Ui4CbOcTmwrmxg1Eoe0= > mk1mb-d...@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.tavak...@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-requ...@gromacs.org. > > > > > ------------------------------ > > Message: 4 > Date: Mon, 29 Oct 2018 13:25:35 +0530 > From: Raag Saluja <saluja.r...@gmail.com> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] Place a gap in y-axis > Message-ID: > <CALwqOC7J99UZmENfwFMoiVQPRJ=G0wYOMxpprFdO-= > 70okz...@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.r...@gmail.com> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] Selection of residues in one of the chains of > heterodimer > Message-ID: > < > calwqoc46omibrpzrjj0b1okkcg5xmmmjoc9nrknzp7bm384...@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.hernan...@chemie.uni-hamburg.de> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Temperature in CG production runs > Message-ID: > <0234af1e-6430-3a9f-683f-5cd5b69d0...@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.hernan...@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-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 174, Issue 71 > ****************************************************** > -- 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-requ...@gromacs.org.