[gmx-users] gromacs.org_gmx-users Digest, Vol 125, Issue 20
Ambarnil Ghosh
ambargromacs at gmail.com
Tue Sep 9 17:59:41 CEST 2014
Thank you very much!
Sincerely
nil
On Thu, Sep 4, 2014 at 2:51 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. adding ions in the genion for multimeric proteins (Ambarnil Ghosh)
> 2. Re: adding ions in the genion for multimeric proteins
> (rajat desikan)
> 3. Re: adding ions in the genion for multimeric proteins
> (Dallas Warren)
> 4. Re: Structuring as function of z - gmx order (Dallas Warren)
> 5. Regarding gromacs installation (Sathya)
> 6. Re: Regarding gromacs installation (Chandan Choudhury)
> 7. Re: Regarding gromacs installation (Chandan Choudhury)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 4 Sep 2014 12:33:34 +0900
> From: Ambarnil Ghosh <ambargromacs at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] adding ions in the genion for multimeric proteins
> Message-ID:
> <
> CAPn+StT-MJZVWQeLxshbZaDebfrEOHjhhto11GfbRqsnqDQHZg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear users,
>
> My protein is a trimer and I want to run md : on binding of a peptide
> (chain-D) to this trimer (chain-ABC).
>
> Therefore, I have four chains. So, when I create topol.top file using
> pdb2gmx it automatically divide the topology in four *.itp files:
> topol_Protein_chain_A.itp
> topol_Protein_chain_B.itp
> topol_Protein_chain_C.itp
> topol_Protein_chain_D.itp
>
> so, in time of running "genion" command its required to mention the number
> of ions to neutralize the protein.
> Now, each of the protein monomer contains net charge of 2 (qtot) in chain
> A, B and C. D-peptide have final qtot as 0.
>
> Now the question is : Where can I get final qtot for whole system? Is it
> like that: I have to just sum up all three (2+2+2) and write "-nn 6" in
> genion command ? Or the final qtot value is written in somewhere else in
> some file, which I missed?
>
> I am new to multimeric simulation, any kind of help/lead is much
> appreciated!
>
> Thanks much
> Sincerely
> Nil
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 4 Sep 2014 09:55:14 +0530
> From: rajat desikan <rajatdesikan at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] adding ions in the genion for multimeric
> proteins
> Message-ID:
> <CA+d_LwtwDuwF-akbU-kQTSX-r7B49+PkQxMW=
> nbYw1XnzG1vBw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Use genion -neutral and let gromacs do that hard work.
>
> Regards,
>
>
> On Thu, Sep 4, 2014 at 9:03 AM, Ambarnil Ghosh <ambargromacs at gmail.com>
> wrote:
>
> > Dear users,
> >
> > My protein is a trimer and I want to run md : on binding of a peptide
> > (chain-D) to this trimer (chain-ABC).
> >
> > Therefore, I have four chains. So, when I create topol.top file using
> > pdb2gmx it automatically divide the topology in four *.itp files:
> > topol_Protein_chain_A.itp
> > topol_Protein_chain_B.itp
> > topol_Protein_chain_C.itp
> > topol_Protein_chain_D.itp
> >
> > so, in time of running "genion" command its required to mention the
> number
> > of ions to neutralize the protein.
> > Now, each of the protein monomer contains net charge of 2 (qtot) in chain
> > A, B and C. D-peptide have final qtot as 0.
> >
> > Now the question is : Where can I get final qtot for whole system? Is it
> > like that: I have to just sum up all three (2+2+2) and write "-nn 6" in
> > genion command ? Or the final qtot value is written in somewhere else in
> > some file, which I missed?
> >
> > I am new to multimeric simulation, any kind of help/lead is much
> > appreciated!
> >
> > Thanks much
> > Sincerely
> > Nil
> > --
> > 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.
> >
>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 04 Sep 2014 03:56:18 +0000
> From: Dallas Warren <Dallas.Warren at monash.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] adding ions in the genion for multimeric
> proteins
> Message-ID:
> <F625AF4746B3A74DACFF00F6F65BECCBC4F851BF at PRK-MBX-04.vcp.local>
> Content-Type: text/plain; charset=us-ascii
>
> When you bundle up the system run file (.tpr), using gmx grompp, to pass
> to gmx genion, it will list in the terminal output the net charge of the
> entire system.
>
> Additionally, you could simply use the -neutral option and not specify the
> number of ions required, the script will work that out for you.
>
> 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
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 04 Sep 2014 03:56:18 +0000
> From: Dallas Warren <Dallas.Warren at monash.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Structuring as function of z - gmx order
> Message-ID:
> <F625AF4746B3A74DACFF00F6F65BECCBC4F851BA at PRK-MBX-04.vcp.local>
> Content-Type: text/plain; charset=us-ascii
>
> Just another pass on this to see if anyone has a comment, with the key
> detail of what I am looking for a response to ...
>
> gmx order
> =========
> Should it be generating the order parameter relative to all three axes
> along a particular axis direction when -noszonly is specified?
>
> Currently it will only generate the one, not all three.
>
> 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
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 4 Sep 2014 10:32:43 +0530
> From: Sathya <bti027.2008 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Regarding gromacs installation
> Message-ID:
> <CAKakSeEnUmeLLQeKPobsjpNfm=
> 9BwOJN7JecVKL5BW-fjSXHkg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi
>
> I have installed cmake version 2.8.12.2 and gromacs 4.6.3 in centOS. During
> installation there was no error. But i didnt get information like Gromacs
> has been successfully installed. When i use pdb2gmx or mdrun commands it is
> showing "command not found". I dont know what is the problem and how should
> i rectify it. Please help me to solve this.
>
>
>
> --
> With regards,
> Sathya.B
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 4 Sep 2014 11:21:08 +0530
> From: Chandan Choudhury <iitdckc at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Regarding gromacs installation
> Message-ID:
> <
> CAHESojw8hWtmmUVFOgXxtYj24-WmwKLtX+X8MaqaXPqOvPSsCg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Follow this link
>
> http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.11._Getting_access_to_GROMACS_after_installation
>
> Chandan
>
>
> On Thu, Sep 4, 2014 at 10:32 AM, Sathya <bti027.2008 at gmail.com> wrote:
>
> > Hi
> >
> > I have installed cmake version 2.8.12.2 and gromacs 4.6.3 in centOS.
> During
> > installation there was no error. But i didnt get information like Gromacs
> > has been successfully installed. When i use pdb2gmx or mdrun commands it
> is
> > showing "command not found". I dont know what is the problem and how
> should
> > i rectify it. Please help me to solve this.
> >
> >
> >
> > --
> > With regards,
> > Sathya.B
> > --
> > 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.
> >
>
>
>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
>
> *"All work and no play makes Jack a dull boy...?*
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 4 Sep 2014 11:21:08 +0530
> From: Chandan Choudhury <iitdckc at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Regarding gromacs installation
> Message-ID:
> <
> CAHESojw8hWtmmUVFOgXxtYj24-WmwKLtX+X8MaqaXPqOvPSsCg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Follow this link
>
> http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.11._Getting_access_to_GROMACS_after_installation
>
> Chandan
>
>
> On Thu, Sep 4, 2014 at 10:32 AM, Sathya <bti027.2008 at gmail.com> wrote:
>
> > Hi
> >
> > I have installed cmake version 2.8.12.2 and gromacs 4.6.3 in centOS.
> During
> > installation there was no error. But i didnt get information like Gromacs
> > has been successfully installed. When i use pdb2gmx or mdrun commands it
> is
> > showing "command not found". I dont know what is the problem and how
> should
> > i rectify it. Please help me to solve this.
> >
> >
> >
> > --
> > With regards,
> > Sathya.B
> > --
> > 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.
> >
>
>
>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
>
> *"All work and no play makes Jack a dull boy...?*
>
>
> ------------------------------
>
> --
> 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 125, Issue 20
> ******************************************************
>
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