Ok, will do. Thanks very much Will > Date: Fri, 11 Feb 2011 13:29:53 -0500 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] Add custom residue to DNA index group > > > > william Stebbeds wrote: > > I made the changes to ../gromacs/top/residuetypes.dat > > > > the Make_ndx output: > > > > 0 System : 34023 atoms > > 1 DNA : 650 atoms > > 2 DGO : 66 atoms > > 3 K : 43 atoms > > 4 CL : 21 atoms > > 5 Other : 66 atoms > > 6 DGO : 66 atoms > > 7 K : 43 atoms > > 8 CL : 21 atoms > > 9 Ion : 64 atoms > > 10 DGO : 66 atoms > > 11 K : 43 atoms > > 12 CL : 21 atoms > > 13 Water : 33243 atoms > > 14 SOL : 33243 atoms > > 15 non-Water : 780 atoms > > 16 Water_and_ions : 33307 atoms > > > > This system consists of a 22 residue DNA molecule, two of which are DGO, > > each have 33 atoms. > > > > I also do not understand why DGO is repeated three times. > > > > There have been significant changes to the generation of default groups for > indexing since the 4.0.x series. I would suggest you upload your input files > and a description of the problem to the Redmine system so it can be > investigated > and fixed. I've seen the same issue with duplicate moleculetypes, which > looks > like it's happening for several species here. It's definitely something > worth > fixing. > > http://redmine.gromacs.org/ > > For now, you can just merge DNA and DGO and create a complete index group. > > -Justin > > > Thanks again > > > > will > > > > > > > Date: Fri, 11 Feb 2011 12:08:52 -0500 > > > From: [email protected] > > > To: [email protected] > > > Subject: Re: [gmx-users] Add custom residue to DNA index group > > > > > > > > > > > > william Stebbeds wrote: > > > > Indeed I did > > > > > > > > DGO DNA > > > > > > > > > > Did you make the change system-wide, or in a local directory? If the > > latter, > > > you have to issue all your commands in that same directory or else > > the default > > > residuetypes.dat (in GMXLIB) will be read. > > > > > > Can you post the make_ndx output (i.e. list of groups)? > > > > > > -Justin > > > > > > > Cheers > > > > > > > > Will > > > > > > > > > Date: Fri, 11 Feb 2011 17:57:32 +0100 > > > > > Subject: RE: [gmx-users] Add custom residue to DNA index group > > > > > From: [email protected] > > > > > To: [email protected] > > > > > > > > > > > > > > > > > Thanks for the quick reply, > > > > > > > > > > > > I have already done that, and GROMACS, in all other cases, > > knows it is > > > > > > DNA, as it automatically forms the bonds with other residues. > > > > > > > > > > > > it is only when it makes its index files that it doesnt know > > that my > > > > > > residue is DNA. > > > > > > > > > > > > > > > > Did you make the change in residuetypes.dat file. > > > > > add your residues XXX as DNA in the residuetypes.dat file > > > > > > > > > > eq: XXX DNA > > > > > > > > > > > > > > > > > > > > Best Wishes, > > > > > > > > > > Sarath > > > > > > Cheers > > > > > > > > > > > > Will > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Date: Sat, 12 Feb 2011 03:33:15 +1100 > > > > > > From: [email protected] > > > > > > To: [email protected] > > > > > > Subject: Re: [gmx-users] Add custom residue to DNA index group > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Message body > > > > > > > > > > > > > > > > > > On 12/02/2011 3:14 AM, william Stebbeds wrote: > > > > > > > > > > > > > > > > > > Hi Folks, > > > > > > > > > > > > > > > > > > > > > > > > I have added a custom DNA residue to the amber99sb ff, and > > > > > > everything works perfectly, (thanks to Justin!). > > > > > > > > > > > > > > > > > > > > > > > > The residue is incorporated perfectly into the sequence, with no > > > > > > abnormal events during simulations. I have updated all the files > > > > > > to include the new residue. > > > > > > > > > > > > > > > > > > > > > > > > I have since realised, when using g_rms, that my custom residue is > > > > > > not included in the default DNA index group, and appears as a > > > > > > group on its own. > > > > > > > > > > > > > > > > > > > > > > > > Is there a way of making gromacs understand that this residue is > > > > > > DNA when it makes the index files? > > > > > > > > > > > > > > > > > > > > > > > > I am not using make_ndx, I just let gromacs split the groups. > > > > > > > > > > > > > > > > > > > > > > > > Thanks in advance > > > > > > > > > > > > > > > > > > > > > > > > Will - Cranfield University > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > You need to arrange for the tools to access a modified form of > > > > > > share/gromacs/top/residuetypes.dat with your custom residue > > suitably > > > > > > classified. I understand you can copy that file to your working > > > > > > directory and modify it there, and GROMACS will use the local copy. > > > > > > > > > > > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > gmx-users mailing list [email protected] > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > > Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > > > Please don't post (un)subscribe requests to the list. Use the > > > > > > www interface or send it to [email protected]. > > > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > > > > > > gmx-users mailing list [email protected] > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > > Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > > > Please don't post (un)subscribe requests to the list. Use the > > > > > > www interface or send it to [email protected]. > > > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > -- > > > > > gmx-users mailing list [email protected] > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > > Please don't post (un)subscribe requests to the list. Use the > > > > > www interface or send it to [email protected]. > > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > -- > > > ======================================== > > > > > > 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 list [email protected] > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [email protected]. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > ======================================== > > 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 list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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