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

[Justin A. Lemkul]

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: 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
>  > >
>  > >
>  > >
>  > >
>  > > --
>  > > gmx-users mailing list gmx-users at 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-request at gromacs.org.
>  > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  > > --
>  > > gmx-users mailing list gmx-users at 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-request at gromacs.org.
>  > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  >
>  >
>  >
>  > --
>  > gmx-users mailing list gmx-users at 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-request at 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

========================================