Re Gromacs NDG BGLC error. Dear Justin
Apologies for not being clearer. NDG was from the crystal structure, CHARM GUI has replaced it with BGLC which is also not recognized. Could you advise me which forcefield would be best for this or how to modify my inputs? Thanks Thomas Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se <gromacs.org_gmx-users-requ...@maillist.sys.kth.se> Sent: Tuesday, March 17, 2020 10:14:53 PM To: gromacs.org_gmx-users@maillist.sys.kth.se <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: gromacs.org_gmx-users Digest, Vol 191, Issue 42 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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=cZCWC%2F257tci0QXNCUKwqlQAJenRX0i8Dp2AQgCKiAw%3D&reserved=0 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. Re: Gromax NDG/BGLC Force field Error (Justin Lemkul) 2. Fwd: Reproducibility of a PMF plot (Alex) 3. Extraction of frames at different interval (Farida Aziz) 4. Re: Fwd: Reproducibility of a PMF plot (Andr? Farias de Moura) 5. About membrane leaflets and msd (Poncho Arvayo Zatarain) 6. About gmx msd and membrane leaflets (Poncho Arvayo Zatarain) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Mar 2020 13:04:08 -0400 From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Gromax NDG/BGLC Force field Error Message-ID: <f2370e1e-374a-aa6f-3d38-222673274...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 3/17/20 12:57 PM, McDonnell, Thomas wrote: > Hey > > I am trying to do some MD of a glycoprotein, I've inputted the glycans > through Charm-GUI online, but when I try to run simulations using any of the > amber or charm forcefields, it throws up the error does not recognise NDG. My > glycan pattern is: > > N-Acetylglucosamine, N-Acetylglucosamine, Mannose (branch) (Mannose, N > Acetylglucosamine, Galactose ) x2 > > How do I modify the input files to overcome this, or is there a different > forcefield I should be using? What is NDG? There is no such residue or patch in the CHARMM force field so I don't know why CHARMM-GUI produced any file with such a residue name. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.thelemkullab.com&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=zMm9lu%2BkBcOf1MR%2FTKd6BqSZHWRYuXSHxin%2Fgz7d8l8%3D&reserved=0 ================================================== ------------------------------ Message: 2 Date: Tue, 17 Mar 2020 13:14:29 -0400 From: Alex <alexanderwie...@gmail.com> To: gmx-us...@gromacs.org Subject: [gmx-users] Fwd: Reproducibility of a PMF plot Message-ID: <CAEDv6u5tnNvtKRAG=f81pqywxgc-4649qzwm6-otycjohca...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Any comment, please? Thank you, Alex ---------- Forwarded message --------- From: Alex <alexanderwie...@gmail.com> Date: Sun, Mar 15, 2020 at 8:16 PM Subject: Reproducibility of a PMF plot To: <gmx-us...@gromacs.org> Dear all, Of course it is always good to prove that a MD simulation is reproducible by repeating several replicas of a simulation and then average over the quantity of interest, specially for a publishable result. I wonder if that also is necessary for a potential of mean force (PMF) calculation using umbrella sampling in which the bootstrap analysis is performed to calculate the standard deviation? Or for an alchemical free energy calculation where the e.g. the block averaging is used? Regards, Alex ------------------------------ Message: 3 Date: Tue, 17 Mar 2020 18:39:11 +0000 (UTC) From: Farida Aziz <faridaazi...@yahoo.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Extraction of frames at different interval Message-ID: <106680237.4263419.1584470351...@mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 ?Hey,?To extract the first frame (t = 0 ns) of the trajectory i have used the below command? gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.pdb -dump 0 ?to extract the frames at 6000 ps, 8600 ps and 9500 ps the following command i adjust like below, are these ok? gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start1.pdb -dump 6000 gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.2pdb -dump 8600 gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start3.pdb -dump 9500 ------------------------------ Message: 4 Date: Tue, 17 Mar 2020 15:10:38 -0300 From: Andr? Farias de Moura <mo...@ufscar.br> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Subject: Re: [gmx-users] Fwd: Reproducibility of a PMF plot Message-ID: <CAKTwKgoP+BPEu1Df0GT_2rp15VySQYW5JdUkeFWVGFfL=tt...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear Alex, in a nutshell: yes, convergence might not have been achieved even if the estimated error bars seem small. maybe this reference might be helpful: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.bbamem.2016.03.006&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=EW1W6sxEg5ZkOxJ67KrQpBoI%2F7JYGTdTkrSZiboQbmA%3D&reserved=0 best, Andre On Tue, Mar 17, 2020 at 2:14 PM Alex <alexanderwie...@gmail.com> wrote: > Any comment, please? > > Thank you, > Alex > > ---------- Forwarded message --------- > From: Alex <alexanderwie...@gmail.com> > Date: Sun, Mar 15, 2020 at 8:16 PM > Subject: Reproducibility of a PMF plot > To: <gmx-us...@gromacs.org> > > > Dear all, > > Of course it is always good to prove that a MD simulation is reproducible > by repeating several replicas of a simulation and then average over the > quantity of interest, specially for a publishable result. > I wonder if that also is necessary for a potential of mean force (PMF) > calculation using umbrella sampling in which the bootstrap analysis is > performed to calculate the standard deviation? > Or for an alchemical free energy calculation where the e.g. the block > averaging is used? > > Regards, > Alex > -- > Gromacs Users mailing list > > * Please search the archive at > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=sgz6a1xlZoQ47DF40KMRMkkwvlXwFkw6HM%2BylpaSjss%3D&reserved=0 > before > posting! > > * Can't post? Read > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=DD%2FRLj4MKlGZ%2BA5uMITT7C6OIoIvBAheONuKckas8pU%3D&reserved=0 > > * For (un)subscribe requests visit > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=cZCWC%2F257tci0QXNCUKwqlQAJenRX0i8Dp2AQgCKiAw%3D&reserved=0 > or > send a mail to gmx-users-requ...@gromacs.org. > -- _____________ Prof. Dr. Andr? Farias de Moura Department of Chemistry Federal University of S?o Carlos S?o Carlos - Brazil phone: +55-16-3351-8090 ------------------------------ Message: 5 Date: Tue, 17 Mar 2020 19:49:31 +0000 From: Poncho Arvayo Zatarain <poncho_8...@hotmail.com> To: "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: [gmx-users] About membrane leaflets and msd Message-ID: <bn6pr08mb3618c7b7ba750901c7eb394580...@bn6pr08mb3618.namprd08.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ?How can separate the leaflets to know wich lipid are in each one? After ?Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd? Thanks ------------------------------ Message: 6 Date: Tue, 17 Mar 2020 22:14:48 +0000 From: Poncho Arvayo Zatarain <poncho_8...@hotmail.com> To: "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: [gmx-users] About gmx msd and membrane leaflets Message-ID: <bn6pr08mb3618a5591a3a882061aa3b7680...@bn6pr08mb3618.namprd08.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ?How can separate the leaflets to know wich lipid are in each one? After ?Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd? Thanks ------------------------------ -- Gromacs Users mailing list * Please search the archive at https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=sgz6a1xlZoQ47DF40KMRMkkwvlXwFkw6HM%2BylpaSjss%3D&reserved=0 before posting! * Can't post? 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