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Ok, will do.<div><br></div><div>Thanks very much</div><div><br></div><div>Will</div><div><br>> Date: Fri, 11 Feb 2011 13:29:53 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Add custom residue to DNA index group<br>> <br>> <br>> <br>> william Stebbeds wrote:<br>> > I made the changes to ../gromacs/top/residuetypes.dat<br>> > <br>> > the Make_ndx output:<br>> > <br>> > 0 System : 34023 atoms<br>> > 1 DNA : 650 atoms<br>> > 2 DGO : 66 atoms<br>> > 3 K : 43 atoms<br>> > 4 CL : 21 atoms<br>> > 5 Other : 66 atoms<br>> > 6 DGO : 66 atoms<br>> > 7 K : 43 atoms<br>> > 8 CL : 21 atoms<br>> > 9 Ion : 64 atoms<br>> > 10 DGO : 66 atoms<br>> > 11 K : 43 atoms<br>> > 12 CL : 21 atoms<br>> > 13 Water : 33243 atoms<br>> > 14 SOL : 33243 atoms<br>> > 15 non-Water : 780 atoms<br>> > 16 Water_and_ions : 33307 atoms<br>> > <br>> > This system consists of a 22 residue DNA molecule, two of which are DGO, <br>> > each have 33 atoms.<br>> > <br>> > I also do not understand why DGO is repeated three times.<br>> > <br>> <br>> There have been significant changes to the generation of default groups for <br>> indexing since the 4.0.x series. I would suggest you upload your input files <br>> and a description of the problem to the Redmine system so it can be investigated <br>> and fixed. I've seen the same issue with duplicate moleculetypes, which looks <br>> like it's happening for several species here. It's definitely something worth <br>> fixing.<br>> <br>> http://redmine.gromacs.org/<br>> <br>> For now, you can just merge DNA and DGO and create a complete index group.<br>> <br>> -Justin<br>> <br>> > Thanks again<br>> > <br>> > will<br>> > <br>> > <br>> > > Date: Fri, 11 Feb 2011 12:08:52 -0500<br>> > > From: jalemkul@vt.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] Add custom residue to DNA index group<br>> > ><br>> > ><br>> > ><br>> > > william Stebbeds wrote:<br>> > > > Indeed I did<br>> > > ><br>> > > > DGO DNA<br>> > > ><br>> > ><br>> > > Did you make the change system-wide, or in a local directory? If the <br>> > latter,<br>> > > you have to issue all your commands in that same directory or else <br>> > the default<br>> > > residuetypes.dat (in GMXLIB) will be read.<br>> > ><br>> > > Can you post the make_ndx output (i.e. list of groups)?<br>> > ><br>> > > -Justin<br>> > ><br>> > > > Cheers<br>> > > ><br>> > > > Will<br>> > > ><br>> > > > > Date: Fri, 11 Feb 2011 17:57:32 +0100<br>> > > > > Subject: RE: [gmx-users] Add custom residue to DNA index group<br>> > > > > From: dsarath@gwdg.de<br>> > > > > To: gmx-users@gromacs.org<br>> > > > ><br>> > > > > ><br>> > > > > > Thanks for the quick reply,<br>> > > > > ><br>> > > > > > I have already done that, and GROMACS, in all other cases, <br>> > knows it is<br>> > > > > > DNA, as it automatically forms the bonds with other residues.<br>> > > > > ><br>> > > > > > it is only when it makes its index files that it doesnt know <br>> > that my<br>> > > > > > residue is DNA.<br>> > > > > ><br>> > > > ><br>> > > > > Did you make the change in residuetypes.dat file.<br>> > > > > add your residues XXX as DNA in the residuetypes.dat file<br>> > > > ><br>> > > > > eq: XXX DNA<br>> > > > ><br>> > > > ><br>> > > > ><br>> > > > > Best Wishes,<br>> > > > ><br>> > > > > Sarath<br>> > > > > > Cheers<br>> > > > > ><br>> > > > > > Will<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > Date: Sat, 12 Feb 2011 03:33:15 +1100<br>> > > > > > From: Mark.Abraham@anu.edu.au<br>> > > > > > To: gmx-users@gromacs.org<br>> > > > > > Subject: Re: [gmx-users] Add custom residue to DNA index group<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > Message body<br>> > > > > ><br>> > > > > ><br>> > > > > > On 12/02/2011 3:14 AM, william Stebbeds wrote:<br>> > > > > ><br>> > > > > ><br>> > > > > > Hi Folks,<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > I have added a custom DNA residue to the amber99sb ff, and<br>> > > > > > everything works perfectly, (thanks to Justin!).<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > The residue is incorporated perfectly into the sequence, with no<br>> > > > > > abnormal events during simulations. I have updated all the files<br>> > > > > > to include the new residue.<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > I have since realised, when using g_rms, that my custom residue is<br>> > > > > > not included in the default DNA index group, and appears as a<br>> > > > > > group on its own.<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > Is there a way of making gromacs understand that this residue is<br>> > > > > > DNA when it makes the index files?<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > I am not using make_ndx, I just let gromacs split the groups.<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > Thanks in advance<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > Will - Cranfield University<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > You need to arrange for the tools to access a modified form of<br>> > > > > > share/gromacs/top/residuetypes.dat with your custom residue <br>> > suitably<br>> > > > > > classified. I understand you can copy that file to your working<br>> > > > > > directory and modify it there, and GROMACS will use the local copy.<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > Mark<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > --<br>> > > > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > > > > Please search the archive at<br>> > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> > > > > > Please don't post (un)subscribe requests to the list. Use the<br>> > > > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> > > > > > --<br>> > > > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > > > > Please search the archive at<br>> > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> > > > > > Please don't post (un)subscribe requests to the list. Use the<br>> > > > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> > > > ><br>> > > > ><br>> > > > ><br>> > > > > --<br>> > > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > > > Please search the archive at<br>> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> > > > > Please don't post (un)subscribe requests to the list. Use the<br>> > > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> > > ><br>> > ><br>> > > --<br>> > > ========================================<br>> > ><br>> > > Justin A. Lemkul<br>> > > Ph.D. Candidate<br>> > > ICTAS Doctoral Scholar<br>> > > MILES-IGERT Trainee<br>> > > Department of Biochemistry<br>> > > Virginia Tech<br>> > > Blacksburg, VA<br>> > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > ><br>> > > ========================================<br>> > > --<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at <br>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? 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