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. Thanks again will > Date: Fri, 11 Feb 2011 12:08:52 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > 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: dsar...@gwdg.de > > > To: gmx-users@gromacs.org > > > > > > > > > > > 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: mark.abra...@anu.edu.au > > > > To: gmx-users@gromacs.org > > > > 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 gmx-users@gromacs.org > > > > 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 gmx-users-requ...@gromacs.org. > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > > > > gmx-users mailing list gmx-users@gromacs.org > > > > 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 gmx-users-requ...@gromacs.org. > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > 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 gmx-users-requ...@gromacs.org. > > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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