[gmx-users] Regarding sg parameter
Hello all, 1. Can anyone help me for making a ndx file for calculating the sg parameter for water? 2. How can i select water between first and second minima of Solvation shells? Thank you -- 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] Regarding LSI calculation
I tried by that. But i was suffering for making .xyz file for my system because I have lots number of frame around 8000. Can you tell me how can I make that kind of fu.XYZ . Thank you On Tue, Nov 19, 2019, 16:23 Christian Blau wrote: > Hi Omar, > > > Though I don't know of any GROMACS tool that can calculate the local > structure index, some third-party tool might help, like > > https://pypi.org/project/iOrder/ > > > The input file format for above tool is .xyz which you can obtain from a > GROMACS trajectory using the MDAnalysis tools here: > > > https://www.mdanalysis.org/docs/documentation_pages/coordinates/XYZ.html#xyz-format > > > Best, > > Christian > > On 11/11/19 4:40 AM, Omkar Singh wrote: > > Hi everyone, > > I want to find out LSI (local structural Index) for my protein water > > system. Can anybody help me regarding this issue? > > > > Thank you > -- > 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] Regarding LSI calculation
Hi everyone, I want to find out LSI (local structural Index) for my protein water system. Can anybody help me regarding this issue? Thank you -- 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] ndx file
Hi everyone, How can I make ndx file for calculating the angle OH-O. Can anyone help regarding this issue? Thank you -- 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] REMD
Hello gmx users, I am getting an error "load imbalance " in remd nvt equilibrium step. Can anyone help me regarding this issue? Thanks -- 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] Index file
Sir, I want to calculate MSD within a cutoff range, how can I wrote a command for that. Can you help me regarding this? Thank you On Wed, Aug 28, 2019, 11:15 Mark Abraham wrote: > Hi, > > There's lots of documentation and examples available. See > > http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#selection-syntax-and-usage > > Mark > > On Wed, 28 Aug 2019 at 07:14, Omkar Singh > wrote: > > > Hi everyone > > Can anyone help me regarding "gmx select" command making a index file > > within a cutoff. > > Thanks > > -- > > 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.
[gmx-users] Index file
Hi everyone Can anyone help me regarding "gmx select" command making a index file within a cutoff. Thanks -- 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] Tetrahedral order parameter
Hello gromacs users, I am working on protein-water system. I am trying to calculate top(tetrahedral order parameter) by "gmx hydorder" command. After finding xpm how to proceed for xvg format. Thanks -- 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] Potential Energy Distribution Plots in REMD
I think you have to give (bandwidth) -bw 0.01 or any number according your data in your command line. On Sat, Aug 10, 2019, 07:45 Shan Jayasinghe wrote: > Dear Gromacs Users, > > I want to plot potential energy distribution plot using the normal > distribution curve (bell curve) for all replicas in my REMD simulation. I > used the command, > > gmx analyze -f Penergy.xvg -dist -normalize > > However, I got a histogram, instead of a bell curve. > Appreciate, if you could help me to get the normalised curve for potential > energy distribution. > > Thank you. > > > > > > -- > Best Regards > Shan Jayasinghe > -- > 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] Cutoff
Hi everyone, I want to calculate gangle within a cutoff region. How can I give cutoff for calculating gmx gangle. Thanks -- 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] MSD
Hi everyone I have a water-protein simulated system. I want to calculate MSD within a cutoff, that thing how can I solve in gromacs. Can anyone help regarding this? Thanks, -- 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] Regarding OH, HH vector distribution
Hello Sir, I want to calculate gangle within a cutoff according my rdf. How can I give cutoff in "gmx gangle... " command line. Can anyone help me regarding this? Thank you, On Thu, Aug 1, 2019, 00:52 David van der Spoel wrote: > Den 2019-07-31 kl. 15:00, skrev Omkar Singh: > > I calculated these two vectors with Z-axis now I want to make > > distribution plot p(costheeta) Vs cos(theeta). How can I plot because it > is > > giving the value only theeta. Is there any command. > Try write your own script. > > Thanks > > > > On Wed, Jul 31, 2019, 12:00 David van der Spoel > > wrote: > > > >> Den 2019-07-31 kl. 06:12, skrev Omkar Singh: > >>> Thanks Sir, > >>> I did like that only, Now how can I make the distribution plot for > these > >>> vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. > >> But > >>> results is not proper. Can you suggest me regarding this? > >>> Thank you > >>> > >> How about gmx gangle -oh ? > >> > >>> > >>> On Tue, Jul 30, 2019, 17:27 David van der Spoel > >>> wrote: > >>> > >>>> Den 2019-07-30 kl. 07:55, skrev Omkar Singh: > >>>>> Hi, > >>>>> I did by "gmx gangle ..." command. But I am not getting good result, > >>>>> because I have a doubt in ndx file. Can you help me for making ndx > >>>> file. > >>>>> How should I select the atom for vectors. > >>>> For OH it should be > >>>> 1 2 > >>>> 1 3 > >>>> 4 5 > >>>> 4 6 > >>>> 7 8 > >>>> 7 9 > >>>> etc., assuming a three particle water model with atoms O H H. > >>>> For HH it should be > >>>> 2 3 > >>>> 5 6 > >>>> 8 9 > >>>> etc. > >>>> A simple script would do it. The dipole vector is somewhat harder. > >>>>> Thanks > >>>>> > >>>>> On Mon, Jul 29, 2019, 22:50 David van der Spoel < > sp...@xray.bmc.uu.se> > >>>>> wrote: > >>>>> > >>>>>> Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > >>>>>>> Hi, > >>>>>>> Meaning is that If I want to calculate angle between OH, HH and dip > >>>>>> vector > >>>>>>> with positive Z-axis. How can I make index file for this issue? And > >> is > >>>> it > >>>>>>> possible that the angle distribution of these vectors for bulk > water > >>>>>>> aproximatly linear. Hope now question is clear. > >>>>>> Probably. Check gmx gangle -g2 z > >>>>>>> > >>>>>>> Thanks > >>>>>>> > >>>>>>> On Mon, Jul 29, 2019, 16:33 David van der Spoel < > >> sp...@xray.bmc.uu.se> > >>>>>>> wrote: > >>>>>>> > >>>>>>>> Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > >>>>>>>>> Hello everyone, > >>>>>>>>> Is it possible that the probability distribution of HH, OH vector > >> for > >>>>>>>> bulk > >>>>>>>>> water is approximately linear? > >>>>>>>>> > >>>>>>>> What do you mean? > >>>>>>>> > >>>>>>>> -- > >>>>>>>> David van der Spoel, Ph.D., Professor of Biology > >>>>>>>> Head of Department, Cell & Molecular Biology, Uppsala University. > >>>>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >>>>>>>> http://www.icm.uu.se > >>>>>>>> -- > >>>>>>>> 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/gromac
[gmx-users] Tetrahedral order parameter
Hi all gmx-users, I have a water-protein simulated system. I want to calculate the Tetrahedral order parameter. Can anybody help me regarding this issue. On Thu, Aug 1, 2019, 00:52 David van der Spoel wrote: > Den 2019-07-31 kl. 15:00, skrev Omkar Singh: > > I calculated these two vectors with Z-axis now I want to make > > distribution plot p(costheeta) Vs cos(theeta). How can I plot because it > is > > giving the value only theeta. Is there any command. > Try write your own script. > > Thanks > > > > On Wed, Jul 31, 2019, 12:00 David van der Spoel > > wrote: > > > >> Den 2019-07-31 kl. 06:12, skrev Omkar Singh: > >>> Thanks Sir, > >>> I did like that only, Now how can I make the distribution plot for > these > >>> vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. > >> But > >>> results is not proper. Can you suggest me regarding this? > >>> Thank you > >>> > >> How about gmx gangle -oh ? > >> > >>> > >>> On Tue, Jul 30, 2019, 17:27 David van der Spoel > >>> wrote: > >>> > >>>> Den 2019-07-30 kl. 07:55, skrev Omkar Singh: > >>>>> Hi, > >>>>> I did by "gmx gangle ..." command. But I am not getting good result, > >>>>> because I have a doubt in ndx file. Can you help me for making ndx > >>>> file. > >>>>> How should I select the atom for vectors. > >>>> For OH it should be > >>>> 1 2 > >>>> 1 3 > >>>> 4 5 > >>>> 4 6 > >>>> 7 8 > >>>> 7 9 > >>>> etc., assuming a three particle water model with atoms O H H. > >>>> For HH it should be > >>>> 2 3 > >>>> 5 6 > >>>> 8 9 > >>>> etc. > >>>> A simple script would do it. The dipole vector is somewhat harder. > >>>>> Thanks > >>>>> > >>>>> On Mon, Jul 29, 2019, 22:50 David van der Spoel < > sp...@xray.bmc.uu.se> > >>>>> wrote: > >>>>> > >>>>>> Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > >>>>>>> Hi, > >>>>>>> Meaning is that If I want to calculate angle between OH, HH and dip > >>>>>> vector > >>>>>>> with positive Z-axis. How can I make index file for this issue? And > >> is > >>>> it > >>>>>>> possible that the angle distribution of these vectors for bulk > water > >>>>>>> aproximatly linear. Hope now question is clear. > >>>>>> Probably. Check gmx gangle -g2 z > >>>>>>> > >>>>>>> Thanks > >>>>>>> > >>>>>>> On Mon, Jul 29, 2019, 16:33 David van der Spoel < > >> sp...@xray.bmc.uu.se> > >>>>>>> wrote: > >>>>>>> > >>>>>>>> Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > >>>>>>>>> Hello everyone, > >>>>>>>>> Is it possible that the probability distribution of HH, OH vector > >> for > >>>>>>>> bulk > >>>>>>>>> water is approximately linear? > >>>>>>>>> > >>>>>>>> What do you mean? > >>>>>>>> > >>>>>>>> -- > >>>>>>>> David van der Spoel, Ph.D., Professor of Biology > >>>>>>>> Head of Department, Cell & Molecular Biology, Uppsala University. > >>>>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >>>>>>>> http://www.icm.uu.se > >>>>>>>> -- > >>>>>>>> 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 >
Re: [gmx-users] Regarding OH, HH vector distribution
I calculated these two vectors with Z-axis now I want to make distribution plot p(costheeta) Vs cos(theeta). How can I plot because it is giving the value only theeta. Is there any command. Thanks On Wed, Jul 31, 2019, 12:00 David van der Spoel wrote: > Den 2019-07-31 kl. 06:12, skrev Omkar Singh: > > Thanks Sir, > > I did like that only, Now how can I make the distribution plot for these > > vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. > But > > results is not proper. Can you suggest me regarding this? > > Thank you > > > How about gmx gangle -oh ? > > > > > On Tue, Jul 30, 2019, 17:27 David van der Spoel > > wrote: > > > >> Den 2019-07-30 kl. 07:55, skrev Omkar Singh: > >>> Hi, > >>> I did by "gmx gangle ..." command. But I am not getting good result, > >>> because I have a doubt in ndx file. Can you help me for making ndx > >> file. > >>> How should I select the atom for vectors. > >> For OH it should be > >> 1 2 > >> 1 3 > >> 4 5 > >> 4 6 > >> 7 8 > >> 7 9 > >> etc., assuming a three particle water model with atoms O H H. > >> For HH it should be > >> 2 3 > >> 5 6 > >> 8 9 > >> etc. > >> A simple script would do it. The dipole vector is somewhat harder. > >>> Thanks > >>> > >>> On Mon, Jul 29, 2019, 22:50 David van der Spoel > >>> wrote: > >>> > >>>> Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > >>>>> Hi, > >>>>> Meaning is that If I want to calculate angle between OH, HH and dip > >>>> vector > >>>>> with positive Z-axis. How can I make index file for this issue? And > is > >> it > >>>>> possible that the angle distribution of these vectors for bulk water > >>>>> aproximatly linear. Hope now question is clear. > >>>> Probably. Check gmx gangle -g2 z > >>>>> > >>>>> Thanks > >>>>> > >>>>> On Mon, Jul 29, 2019, 16:33 David van der Spoel < > sp...@xray.bmc.uu.se> > >>>>> wrote: > >>>>> > >>>>>> Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > >>>>>>> Hello everyone, > >>>>>>> Is it possible that the probability distribution of HH, OH vector > for > >>>>>> bulk > >>>>>>> water is approximately linear? > >>>>>>> > >>>>>> What do you mean? > >>>>>> > >>>>>> -- > >>>>>> David van der Spoel, Ph.D., Professor of Biology > >>>>>> Head of Department, Cell & Molecular Biology, Uppsala University. > >>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >>>>>> http://www.icm.uu.se > >>>>>> -- > >>>>>> 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. > >>>>>> > >>>> > >>>> > >>>> -- > >>>> David van der Spoel, Ph.D., Professor of Biology > >>>> Head of Department, Cell & Molecular Biology, Uppsala University. > >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >>>> http://www.icm.uu.se > >>>> -- > >>>> 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] Regarding OH, HH vector distribution
Thanks Sir, I did like that only, Now how can I make the distribution plot for these vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But results is not proper. Can you suggest me regarding this? Thank you On Tue, Jul 30, 2019, 17:27 David van der Spoel wrote: > Den 2019-07-30 kl. 07:55, skrev Omkar Singh: > > Hi, > > I did by "gmx gangle ..." command. But I am not getting good result, > > because I have a doubt in ndx file. Can you help me for making ndx > file. > > How should I select the atom for vectors. > For OH it should be > 1 2 > 1 3 > 4 5 > 4 6 > 7 8 > 7 9 > etc., assuming a three particle water model with atoms O H H. > For HH it should be > 2 3 > 5 6 > 8 9 > etc. > A simple script would do it. The dipole vector is somewhat harder. > > Thanks > > > > On Mon, Jul 29, 2019, 22:50 David van der Spoel > > wrote: > > > >> Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > >>> Hi, > >>> Meaning is that If I want to calculate angle between OH, HH and dip > >> vector > >>> with positive Z-axis. How can I make index file for this issue? And is > it > >>> possible that the angle distribution of these vectors for bulk water > >>> aproximatly linear. Hope now question is clear. > >> Probably. Check gmx gangle -g2 z > >>> > >>> Thanks > >>> > >>> On Mon, Jul 29, 2019, 16:33 David van der Spoel > >>> wrote: > >>> > >>>> Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > >>>>> Hello everyone, > >>>>> Is it possible that the probability distribution of HH, OH vector for > >>>> bulk > >>>>> water is approximately linear? > >>>>> > >>>> What do you mean? > >>>> > >>>> -- > >>>> David van der Spoel, Ph.D., Professor of Biology > >>>> Head of Department, Cell & Molecular Biology, Uppsala University. > >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >>>> http://www.icm.uu.se > >>>> -- > >>>> 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. > >>>> > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> 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. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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] Regarding OH, HH vector distribution
Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I select the atom for vectors. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: > Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > > Hi, > > Meaning is that If I want to calculate angle between OH, HH and dip > vector > > with positive Z-axis. How can I make index file for this issue? And is it > > possible that the angle distribution of these vectors for bulk water > > aproximatly linear. Hope now question is clear. > Probably. Check gmx gangle -g2 z > > > > Thanks > > > > On Mon, Jul 29, 2019, 16:33 David van der Spoel > > wrote: > > > >> Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > >>> Hello everyone, > >>> Is it possible that the probability distribution of HH, OH vector for > >> bulk > >>> water is approximately linear? > >>> > >> What do you mean? > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> 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. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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] Regarding OH, HH vector distribution
Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: > Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > > Hello everyone, > > Is it possible that the probability distribution of HH, OH vector for > bulk > > water is approximately linear? > > > What do you mean? > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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] Regarding OH, HH vector distribution
Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? -- 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] Angular distribution
Hi everyone, I have a protein Water simulated system and I want to calculate Angular distribution function. How can I find can anyone help me with this? Thanks -- 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] Tetrahedral order
Thanks Sir, But it is giving the xpm file. How can I get xvg file? On Wed, Jul 10, 2019, 06:51 Justin Lemkul wrote: > > > On 7/9/19 4:24 AM, Omkar Singh wrote: > > Dear all, > > I want to calculate the Tetrahedral order parameter through gmx. Can > anyone > > help? Eventhough I tried but my system has 500 water molecules Fir that I > > am unable to make index file because it will take lots of time for typing > > any suggestions. Commend > > gmx order -f .xtc -s .tpr -b 0 -e 1 -n .ndx -nr .ndx -d y > -permolecule > > You're using the wrong tool. gmx order is explicitly for carbon atoms, > e.g. alkyl chains in phospholipids. You want gmx hydorder. > > -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 > http://www.thelemkullab.com > > == > > -- > 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] Tetrahedral order
Dear all, I want to calculate the Tetrahedral order parameter through gmx. Can anyone help? Eventhough I tried but my system has 500 water molecules Fir that I am unable to make index file because it will take lots of time for typing any suggestions. Commend gmx order -f .xtc -s .tpr -b 0 -e 1 -n .ndx -nr .ndx -d y -permolecule -- 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] Water Density
Hello everyone I did a protein water simulation. I want to calculate water density in both interface and bulk. How can I find this resulte? Thanks -- 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] Regarding Simulation
Hello gromacs users, I am doing protein-water simulation with calculating velocity. I am getting thins kind of checkpoint files, Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.92508e+031.15716e+036.91130e+02 -1.22494e+021.70241e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 9.37486e+04 -2.58204e+03 -6.26105e+051.62962e+03 -5.12634e+05 Kinetic En. Total Energy Conserved En.Temperature Pres. DC (bar) 8.23638e+04 -4.30270e+05 -1.00795e+062.97016e+02 -1.27048e+02 Pressure (bar) Constr. rmsd -1.49490e+022.24907e-05 Writing checkpoint, step 89675360 at Sun May 26 08:34:47 2019 Writing checkpoint, step 89679840 at Sun May 26 08:49:54 2019 Writing checkpoint, step 89684160 at Sun May 26 09:04:53 2019 Writing checkpoint, step 89688640 at Sun May 26 09:19:57 2019 Writing checkpoint, step 89693200 at Sun May 26 09:34:45 2019 Writing checkpoint, step 89697280 at Sun May 26 09:50:18 2019, Why it is happening? Can any tell? Thanks -- 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] Regarding to find coordination number
Dear Experts, I performed a protein-water simulation in gromacs 2018.4. Now i am concentrating to find the coordination number of Oxygen atom of water molecule in whole system. Kindly help me to solve this problem. Thanks -- 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] control parameter on the Lennard-Jones interactions
I have protein MD simulation file I want to find out protein water rdf with coordination number. Can anyone help regarding this? Thanks On Thu, May 16, 2019, 10:55 wrote: > > Dear gromacs members, > > I would ask you if in gromacs is possible to add a control parameter on > the Lennard-Jones interactions. > For example we have two atoms A and B and the corresponding parameters; > sigma(A), eps(A), sigma(B), esp(B); then for the A-B interactions we have > the parameters obtained with the Lorentz-Berthelot or with the geometrical > average. > > I would like to have a standard interaction between A or B with the other > atoms of the system. In the same time I would like to add a control > parameter C on the interaction between A and B to have the following > potential: > V(r(AB))=4*eps(AB)*[(sigma(AB)/r(AB))^(12)-C*(sigma(AB)/r(AB))^(6)] > > Is it possible? How can I manage this calculation? > > > Many thanks, > > > Anna > > > > > -- > 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] regarding editconf
My advice is that don't use many option in on shot. In place of -center try by -translate with rotation. Best regard On Tue, Jan 15, 2019 at 8:52 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Thank you Justin. I try to search more for the reason. My best, Ali > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > On Behalf Of Justin > Lemkul > Sent: dinsdag 15 januari 2019 16:10 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] regarding editconf > > > > On 1/15/19 9:34 AM, Ali Khodayari wrote: > > Thank you for your response Justin! > > I don't really see how it can cause an error, while it might be just a > > visualization defect in VMD. > > Previously, I tried to perform each step separately, like doing a > > centering by -center 0 0 0, but even performing this step leads to the > error "step 0: > > Water molecule starting at atom 40225 can not be settled." The only > > difference would be a change in the coordinates, no? It is not due to > > the fact that I am using 5.1.2 version, is it? > > Systems can become unstable for any number of reasons, but not simply > because some part of a protein appears to be protruding into space. > That's just normal PBC. > > 5.1.2 is very old but I don't know of any specific reason why it should > cause a problem. > > -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 > http://www.thelemkullab.com > > == > > -- > 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.
[gmx-users] Regarding self-assembly of Peptides
Hi, I have a peptide (capped peptide) and i want to do the self assembly in GROMACS. So, may i know how to do this self assembly in gromacs..?? Any suggestions..? Thank you. -- 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] Capping of peptide terminal ends
Hi , I did same as you suggest me, but now new error is coming as shown below. I just backed up topol.top to ./#topol.top.30# Processing chain 1 (64 atoms, 7 residues) Identified residue ACE0 as a starting terminus. Identified residue CT31 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for ACE-0 0: NH3+ 1: NH2 2: None 2 Start terminus ACE-0: None Select end terminus type for CT3-1 0: CT3 1: COO- 2: COOH 3: CT2 4: None 4 End terminus CT3-1: None Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.arn Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.arn Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.arn --- Program: gmx pdb2gmx, version 2016.2 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753) Fatal error: Atom H31 in residue ACE 0 was not found in rtp entry ACE with 6 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors terminal entries are as following N-terminal ATOM 3 CH3 ACE 0 8.735 -0.604 2.523 1.00 0.00 C ATOM 31 H31 ACE 0 9.608 0.044 2.605 1.00 0.00 H ATOM 32 H32 ACE 0 8.348 -0.783 3.526 1.00 0.00 H ATOM 33 H33 ACE 0 9.056 -1.553 2.095 1.00 0.00 H ATOM 2 C ACE 1 7.677 0.041 1.642 1.00 0.00 C ATOM 4 O ACE 1 7.890 1.122 1.099 1.00 0.00 O C- terminal ATOM 23 N CT3 1 -5.561 0.819 -3.047 1.00 0.00 N ATOM 50 HN CT3 1 -5.240 1.762 -2.900 1.00 0.00 H ATOM 24 CH3 CT3 1 -6.804 0.635 -3.787 1.00 0.00 C ATOM 51 H31 CT3 1 -7.250 1.599 -4.034 1.00 0.00 H ATOM 52 H32 CT3 1 -6.624 0.095 -4.718 1.00 0.00 H ATOM 53 H33 CT3 1 -7.527 0.065 -3.201 1.00 0.00 H The spacing is fine in real pdb. On Fri, Oct 12, 2018 at 8:36 PM Justin Lemkul wrote: > > > On 10/12/18 6:35 AM, Omkar Singh wrote: > > Hi all, > > I have a peptide system with capinng, N-ACE and C-NAC. i would like to > > create a topology file .I tried with pdb2gmx script but it is showing a > > fatal error like as; > > Fatal error: > > atom N not found in buiding block 1ACE while combining tdb and rtp. I > > already tried by editing in .rtp entry but after that it is showing > error. > > I am using CHARMM27 ff/ > > Select the Force Field: > > From '/usr/local/gromacs/share/gromacs/top': > > 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, > > 1999-2012, 2003) > > 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) > > 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. > 29, > > 461-469, 1996) > > 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, > > 1049-1074, 2000) > > 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, > > 712-725, 2006) > > 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., > > Proteins 78, 1950-58, 2010) > > 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) > > 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) > > 9: CHARMM36 all-atom force field (March 2017) > > 10: GROMOS96 43a1 force field > > 11: GROMOS96 43a2 force field (improved alkane dihedrals) > > 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) > > 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) > > 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > > 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, > DOI: > > 10.1007/s00249-011-0700-9) > > 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) > > 8 > > > > Using the Charmm27 force field in directory charmm27.ff > > > > Opening force field file > > /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b > > Opening force field file > > /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b > > Reading a3k1.pdb... > > Read 'Stru
[gmx-users] Capping of peptide terminal ends
Hi all, I have a peptide system with capinng, N-ACE and C-NAC. i would like to create a topology file .I tried with pdb2gmx script but it is showing a fatal error like as; Fatal error: atom N not found in buiding block 1ACE while combining tdb and rtp. I already tried by editing in .rtp entry but after that it is showing error. I am using CHARMM27 ff/ Select the Force Field: >From '/usr/local/gromacs/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 9: CHARMM36 all-atom force field (March 2017) 10: GROMOS96 43a1 force field 11: GROMOS96 43a2 force field (improved alkane dihedrals) 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9) 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 8 Using the Charmm27 force field in directory charmm27.ff Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b Reading a3k1.pdb... Read 'Structure1', 64 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 6 residues with 64 atoms chain #res #atoms 1 ' ' 6 64 All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp Atomtype 213 Reading residue database... (charmm27) Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp Residue 44 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp Residue 48 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp Residue 60 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp Residue 64 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.8# Processing chain 1 (64 atoms, 6 residues) Identified residue ACE1 as a starting terminus. Identified residue CT35 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Start terminus ACE-1: NH3+ End terminus CT3-5: CT3 --- Program: gmx pdb2gmx, version 2016.2 Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1127) Fatal error: atom N not found in buiding block 1ACE while combining tdb and rtp I'll be greatfull for any kind of suggestions. -- 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.
