Thank you very much! Sincerely nil On Thu, Sep 4, 2014 at 2:51 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. 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 <ambargrom...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] adding ions in the genion for multimeric proteins > Message-ID: > < > capn+stt-mjzvwqelxshbzadebfreohjhhto11gfbrqsnqdq...@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 <rajatdesi...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] adding ions in the genion for multimeric > proteins > Message-ID: > <CA+d_LwtwDuwF-akbU-kQTSX-r7B49+PkQxMW= > nbyw1xnzg1...@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 <ambargrom...@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-requ...@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.war...@monash.edu> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] adding ions in the genion for multimeric > proteins > Message-ID: > <f625af4746b3a74dacff00f6f65beccbc4f85...@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.war...@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.war...@monash.edu> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] Structuring as function of z - gmx order > Message-ID: > <f625af4746b3a74dacff00f6f65beccbc4f85...@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.war...@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 <bti027.2...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Regarding gromacs installation > Message-ID: > <CAKakSeEnUmeLLQeKPobsjpNfm= > 9bwojn7jecvkl5bw-fjsx...@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 <iitd...@gmail.com> > To: gmx-users <gmx-us...@gromacs.org> > Cc: Discussion list for GROMACS users > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: Re: [gmx-users] Regarding gromacs installation > Message-ID: > < > cahesojw8hwtmmuvfogxxtyj24-wmwkltx+x8maqaxpqovps...@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 <bti027.2...@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-requ...@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 <iitd...@gmail.com> > To: gmx-users <gmx-us...@gromacs.org> > Cc: Discussion list for GROMACS users > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: Re: [gmx-users] Regarding gromacs installation > Message-ID: > < > cahesojw8hwtmmuvfogxxtyj24-wmwkltx+x8maqaxpqovps...@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 <bti027.2...@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-requ...@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-requ...@gromacs.org. > > > End of gromacs.org_gmx-users Digest, Vol 125, Issue 20 > ****************************************************** > -- 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.