[gmx-users] Add custom residue to DNA index group

[william Stebbeds]

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: dsarath at gwdg.de
> To: gmx-users at 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.Abraham at anu.edu.au
> > To: gmx-users at 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
> >
> >
> >
> >
> > --
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> 
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