Re: [gmx-users] i have queston about partial charge zinc
The original online server at the University of Cambridge has been retired after almost 8 years of service I'm sorry. The machine there was really outdated and impossible to update ACPYPE with new features we've developed in the past couple of years. We are working to have the new one up and running but unfortunately I can predict a date for the return. For sure, we will announce in the proper channels when the new server is up. Sorry for the inconvenience, Alan On Sun, 30 Sep 2018 at 09:11, neelam wafa wrote: > Hi ! > Alan the link for updated acpype you have shared is all about the > downloadable tool. Can you please share the link for online server for > it. and is their any tutorial to explain the changed protocol. > looking forward for your cooperation. > > Regards > > On 9/20/18, Alan wrote: > > Please, official, original, updated ACPYPE is now here: > > https://github.com/alanwilter/acpype > > > > Alan > > > > On 20 September 2018 at 13:56, Andrea Coletta > > > wrote: > > > >> In general I would say that +2 is not a good choice, since it seems to > me > >> that this is a Zinc complex. > >> > >> You may want to look at this: > >> > >> http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm > >> > >> you should be able to create the topology in ambertools and then convert > >> it to gromac with acpype (https://github.com/llazzaro/acpype) > >> > >> -Original Message- > >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of milad > >> bagheri > >> Sent: 20. september 2018 14:28 > >> To: gromacs.org_gmx-users@maillist.sys.kth.se > >> Subject: [gmx-users] i have queston about partial charge zinc > >> > >> Hi > >> I gonna MD simulation a protein that contained a zinc ion for build > >> topology I used from the amber99sb force field Atomic charge is written > >> "+2" in topology. > >> I wanted to ask if this charge is correct or should be calculated in a > >> different way? > >> "PDB id 4row" > >> sincerely > >> -- > >> 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. > >> -- > >> 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. > >> > > > > > > > > -- > > I'll cycle across Britain in 2018 for a charity, would you consider > > supporting my cause? http://uk.virginmoneygiving.com/AlanSilva > > Many thanks! > > -- > > Alan Wilter SOUSA da SILVA, DSc > > Senior Bioinformatician, UniProt > > European Bioinformatics Institute (EMBL-EBI) > > European Molecular Biology Laboratory > > Wellcome Trust Genome Campus > > Hinxton > > Cambridge CB10 1SD > > United Kingdom > > Tel: +44 (0)1223 494588 > > -- > > 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. > > > -- > 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. > -- *I** have just cycled* from Land's End to John O'Groats (the whole Britain!) for a charity, would you consider supporting my cause? http://uk.virginmoneygiving.com/AlanSilva -- Alan Wilter SOUSA da SILVA, DSc Senior Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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.
Re: [gmx-users] i have queston about partial charge zinc
Hi ! Alan the link for updated acpype you have shared is all about the downloadable tool. Can you please share the link for online server for it. and is their any tutorial to explain the changed protocol. looking forward for your cooperation. Regards On 9/20/18, Alan wrote: > Please, official, original, updated ACPYPE is now here: > https://github.com/alanwilter/acpype > > Alan > > On 20 September 2018 at 13:56, Andrea Coletta > wrote: > >> In general I would say that +2 is not a good choice, since it seems to me >> that this is a Zinc complex. >> >> You may want to look at this: >> >> http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm >> >> you should be able to create the topology in ambertools and then convert >> it to gromac with acpype (https://github.com/llazzaro/acpype) >> >> -Original Message- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of milad >> bagheri >> Sent: 20. september 2018 14:28 >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] i have queston about partial charge zinc >> >> Hi >> I gonna MD simulation a protein that contained a zinc ion for build >> topology I used from the amber99sb force field Atomic charge is written >> "+2" in topology. >> I wanted to ask if this charge is correct or should be calculated in a >> different way? >> "PDB id 4row" >> sincerely >> -- >> 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. >> -- >> 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. >> > > > > -- > I'll cycle across Britain in 2018 for a charity, would you consider > supporting my cause? http://uk.virginmoneygiving.com/AlanSilva > Many thanks! > -- > Alan Wilter SOUSA da SILVA, DSc > Senior Bioinformatician, UniProt > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Tel: +44 (0)1223 494588 > -- > 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. > -- 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.
Re: [gmx-users] i have queston about partial charge zinc
Please, official, original, updated ACPYPE is now here: https://github.com/alanwilter/acpype Alan On 20 September 2018 at 13:56, Andrea Coletta wrote: > In general I would say that +2 is not a good choice, since it seems to me > that this is a Zinc complex. > > You may want to look at this: > > http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm > > you should be able to create the topology in ambertools and then convert > it to gromac with acpype (https://github.com/llazzaro/acpype) > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of milad > bagheri > Sent: 20. september 2018 14:28 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] i have queston about partial charge zinc > > Hi > I gonna MD simulation a protein that contained a zinc ion for build > topology I used from the amber99sb force field Atomic charge is written > "+2" in topology. > I wanted to ask if this charge is correct or should be calculated in a > different way? > "PDB id 4row" > sincerely > -- > 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. > -- > 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. > -- I'll cycle across Britain in 2018 for a charity, would you consider supporting my cause? http://uk.virginmoneygiving.com/AlanSilva Many thanks! -- Alan Wilter SOUSA da SILVA, DSc Senior Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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.
Re: [gmx-users] i have queston about partial charge zinc
In general I would say that +2 is not a good choice, since it seems to me that this is a Zinc complex. You may want to look at this: http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm you should be able to create the topology in ambertools and then convert it to gromac with acpype (https://github.com/llazzaro/acpype) -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of milad bagheri Sent: 20. september 2018 14:28 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] i have queston about partial charge zinc Hi I gonna MD simulation a protein that contained a zinc ion for build topology I used from the amber99sb force field Atomic charge is written "+2" in topology. I wanted to ask if this charge is correct or should be calculated in a different way? "PDB id 4row" sincerely -- 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. -- 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.
[gmx-users] i have queston about partial charge zinc
Hi I gonna MD simulation a protein that contained a zinc ion for build topology I used from the amber99sb force field Atomic charge is written "+2" in topology. I wanted to ask if this charge is correct or should be calculated in a different way? "PDB id 4row" sincerely -- 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.
