> > 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
