Re: [gmx-users] Is it possible to generate lipid.itp with Charmm36 ff?
On 4/7/15 4:29 PM, Yunlong Liu wrote: Hi Micholas, I will try it but last time when I tried, the charm-Gui was not working. If you have some specific problem, you should report it to the CHARMM-GUI team. Unfortunately "not working" is not a helpful diagnosis. Things should be fully operational and have been for a long time. -Justin Yunlong Sent from my iPhone On Apr 7, 2015, at 4:21 PM, Smith, Micholas D. wrote: If you mean you want to set up the system for using Charmm36's parameters, you might be able to use the Charmm-GUI (Wonpil Im's group) -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Yunlong Liu Sent: Tuesday, April 07, 2015 4:18 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Is it possible to generate lipid.itp with Charmm36 ff? Hi, I am doing membrane-protein simulation with Charmm36 forcefield. I would like to know whether I can generate the lipid force field with Charmm36 by some available tools? Yunlong -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Is it possible to generate lipid.itp with Charmm36 ff?
Hi Micholas, I will try it but last time when I tried, the charm-Gui was not working. Yunlong Sent from my iPhone > On Apr 7, 2015, at 4:21 PM, Smith, Micholas D. wrote: > > If you mean you want to set up the system for using Charmm36's parameters, > you might be able to use the Charmm-GUI (Wonpil Im's group) > > -Micholas > > === > Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Yunlong Liu > > Sent: Tuesday, April 07, 2015 4:18 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Is it possible to generate lipid.itp with Charmm36 ff? > > Hi, > > I am doing membrane-protein simulation with Charmm36 forcefield. I would > like to know whether I can generate the lipid force field with Charmm36 > by some available tools? > > Yunlong > -- > 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. -- 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] Is it possible to generate lipid.itp with Charmm36 ff?
On 4/7/15 4:44 PM, Yunlong Liu wrote: Oh I see. I saw the website this afternoon. Do you refer to the package charmm36-nov2014? I checked the file inside but see no dppc or popc entry inside. I just want to make sure whether it can work for popc membrane? Yes. I ask this since I don't quite understand how the lipid membrane force field top files should be correctly represented in GROMACS. I read your tutorial and see you are talking about "lipid.itp". Different force fields, different approaches. I would encourage you to follow Micholas' advice and proceed through CHARMM-GUI. It will even build the entire membrane for you if you want, as well as provide all of the inputs (.mdp) with correct settings (including things that people frequently screw up). We don't provide individual molecule .itp files for lipids. They are all .rtp entries, so you can process the structure directly with pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Is it possible to generate lipid.itp with Charmm36 ff?
Oh I see. I saw the website this afternoon. Do you refer to the package charmm36-nov2014? I checked the file inside but see no dppc or popc entry inside. I just want to make sure whether it can work for popc membrane? I ask this since I don't quite understand how the lipid membrane force field top files should be correctly represented in GROMACS. I read your tutorial and see you are talking about "lipid.itp". Thank you. Yunlong > On Apr 7, 2015, at 4:37 PM, Justin Lemkul wrote: > > >> On 4/7/15 4:27 PM, Yunlong Liu wrote: >> Hi Justin, >> >> I mean I would like to set it up with Charmm36. The provided one is under >> OPLS and gromos ff. > > Visit the link I posted. Our force field files have nothing to do with OPLS > or GROMOS. There is no such thing as "lipid.itp" for CHARMM36; that commonly > refers to the Berger parameters, as distributed by Peter Tieleman's group. > > -Justin > >> Yunlong >> >>> On Apr 7, 2015, at 4:20 PM, Justin Lemkul wrote: >>> >>> >>> On 4/7/15 4:18 PM, Yunlong Liu wrote: Hi, I am doing membrane-protein simulation with Charmm36 forcefield. I would like to know whether I can generate the lipid force field with Charmm36 by some available tools? >>> >>> No need to generate anything. We provide the whole force field here: >>> >>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> 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. > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] Is it possible to generate lipid.itp with Charmm36 ff?
On 4/7/15 4:27 PM, Yunlong Liu wrote: Hi Justin, I mean I would like to set it up with Charmm36. The provided one is under OPLS and gromos ff. Visit the link I posted. Our force field files have nothing to do with OPLS or GROMOS. There is no such thing as "lipid.itp" for CHARMM36; that commonly refers to the Berger parameters, as distributed by Peter Tieleman's group. -Justin Yunlong On Apr 7, 2015, at 4:20 PM, Justin Lemkul wrote: On 4/7/15 4:18 PM, Yunlong Liu wrote: Hi, I am doing membrane-protein simulation with Charmm36 forcefield. I would like to know whether I can generate the lipid force field with Charmm36 by some available tools? No need to generate anything. We provide the whole force field here: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Is it possible to generate lipid.itp with Charmm36 ff?
Hi Justin, I mean I would like to set it up with Charmm36. The provided one is under OPLS and gromos ff. Yunlong > On Apr 7, 2015, at 4:20 PM, Justin Lemkul wrote: > > > >> On 4/7/15 4:18 PM, Yunlong Liu wrote: >> Hi, >> >> I am doing membrane-protein simulation with Charmm36 forcefield. I would >> like to >> know whether I can generate the lipid force field with Charmm36 by some >> available tools? > > No need to generate anything. We provide the whole force field here: > > http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] Is it possible to generate lipid.itp with Charmm36 ff?
If you mean you want to set up the system for using Charmm36's parameters, you might be able to use the Charmm-GUI (Wonpil Im's group) -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Yunlong Liu Sent: Tuesday, April 07, 2015 4:18 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Is it possible to generate lipid.itp with Charmm36 ff? Hi, I am doing membrane-protein simulation with Charmm36 forcefield. I would like to know whether I can generate the lipid force field with Charmm36 by some available tools? Yunlong -- 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] Is it possible to generate lipid.itp with Charmm36 ff?
On 4/7/15 4:18 PM, Yunlong Liu wrote: Hi, I am doing membrane-protein simulation with Charmm36 forcefield. I would like to know whether I can generate the lipid force field with Charmm36 by some available tools? No need to generate anything. We provide the whole force field here: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Is it possible to generate lipid.itp with Charmm36 ff?
Hi, I am doing membrane-protein simulation with Charmm36 forcefield. I would like to know whether I can generate the lipid force field with Charmm36 by some available tools? Yunlong -- 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.
