Re: [gmx-users] DPPC to CG DPPC
For the steps to go through to have an embedded protein in membrane bilayer Justin has made a nice tutorial ... look in the mail list archive On Dec 15, 2009, at 6:21 PM, sunny mishra wrote: ok. Thats the step where I am really confused that how to apply the PR on my system file (system file is a combination of CG protein and CG lipid). On Tue, Dec 15, 2009 at 12:16 PM, XAvier Periole wrote: Well if you put a protein CG into your DPPC bilayer you'll have to be soft on the start. PR is one way to do it and you can do similar to when doing on a atomistic simulation. On Dec 15, 2009, at 6:13 PM, sunny mishra wrote: Alright thanks. So should I do it for proteins? On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole wrote: No need of position restrained simulation with the CG lipids. CG is very forgiving :)) For proteins it is more delicate. On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole wrote: I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
ok. Thats the step where I am really confused that how to apply the PR on my system file (system file is a combination of CG protein and CG lipid). On Tue, Dec 15, 2009 at 12:16 PM, XAvier Periole wrote: > > Well if you put a protein CG into your DPPC bilayer you'll have to > be soft on the start. PR is one way to do it and you can do similar > to when doing on a atomistic simulation. > > On Dec 15, 2009, at 6:13 PM, sunny mishra wrote: > > Alright thanks. So should I do it for proteins? > > On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole wrote: > >> >> No need of position restrained simulation with the CG lipids. >> CG is very forgiving :)) >> >> For proteins it is more delicate. >> >> On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: >> >> Thanks for the reply. I have another quick question that If I have to do >> the Position Restrained EM Simulation of CG DPPC lipid then is it done the >> same way we do for atomistic structure of proteins like by defining the >> LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there >> any other way of doing the Position Restrained EM simulation of CG DPPC >> lipids? >> >> On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole wrote: >> >>> I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... >>> >>> I would suggest you take dppc structure file from the martini web site! >>> >>> Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use thewww >>> interface or send it to gmx-users-requ...@gromacs.org. >>> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
Well if you put a protein CG into your DPPC bilayer you'll have to be soft on the start. PR is one way to do it and you can do similar to when doing on a atomistic simulation. On Dec 15, 2009, at 6:13 PM, sunny mishra wrote: Alright thanks. So should I do it for proteins? On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole wrote: No need of position restrained simulation with the CG lipids. CG is very forgiving :)) For proteins it is more delicate. On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole wrote: I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
Alright thanks. So should I do it for proteins? On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole wrote: > > No need of position restrained simulation with the CG lipids. > CG is very forgiving :)) > > For proteins it is more delicate. > > On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: > > Thanks for the reply. I have another quick question that If I have to do > the Position Restrained EM Simulation of CG DPPC lipid then is it done the > same way we do for atomistic structure of proteins like by defining the > LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there > any other way of doing the Position Restrained EM simulation of CG DPPC > lipids? > > On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole wrote: > >> I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website >>> and I am trying to convert the Atomistic structure to CG structure. For that >>> I am using atom2cg script provided by the martini folks but it doesn't >>> convert the Atomistic structure to CG structure. atom2cg script works well >>> for converting the atomistic structure of PROTEIN to CG structure of protein >>> but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 >>> DPPC atomistic structure of lipids to CG structure. >>> >>> This is correct. atom2cg is only working for proteins ... >> >> I would suggest you take dppc structure file from the martini web site! >> >> Best Regards, >>> >>> Sunny >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use thewww interface >> or send it to gmx-users-requ...@gromacs.org. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
No need of position restrained simulation with the CG lipids. CG is very forgiving :)) For proteins it is more delicate. On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole wrote: I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole wrote: > I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website >> and I am trying to convert the Atomistic structure to CG structure. For that >> I am using atom2cg script provided by the martini folks but it doesn't >> convert the Atomistic structure to CG structure. atom2cg script works well >> for converting the atomistic structure of PROTEIN to CG structure of protein >> but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 >> DPPC atomistic structure of lipids to CG structure. >> >> This is correct. atom2cg is only working for proteins ... > > I would suggest you take dppc structure file from the martini web site! > > Best Regards, >> >> Sunny >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
sunny mishra wrote: Dear All, I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does Right, because it's designed specifically for proteins. anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. There is no need. On the MARTINI site, they offer several pre-equilibrated CG lipid membranes, suitable topologies, etc. -Justin Best Regards, Sunny -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
