Indeed I did DGO DNA
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
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